Start off by starting a new map. For this demonstration, I am going to use the map New York, but this guide works for any of the included maps.
The first thing I would do is pause the game (by pressing Spacebar) to give you time to think and plan.

I would then look at the given starting layout, and change it so that I have two platforms at the sink (which we will refer to as A) - some maps already have this such as New York, but some don't. We need one platform at the in-map station (which we will refer to as B), all starting maps already have this, and ideally we need a double track to just outside station B. This might be easier said than done on some maps, as initial cash flow might be limiting, so run a less intensive train service until you get the funds to build the tracks as desired.

Again, if funds allow, put a manual signal on the approach to both stations, to give us:
Sell any Conductors and Dispatchers Offices already on the map, and then find a place near one of the stations that doesn't have platforms/signs/existing track to build some. Buy as many as your money allows (you can sell them back at full price when you don't need them or when you need money).
On some maps, this might only be one or two conductors offices at this point, that'll work, just build more as and when you start making money.

All maps include starter contracts, but I'd recommend either updating them, or even cancelling them all and starting from scratch. To see what you have to begin with, click on the Contracts button (or press the I key)
If you want to delete all the starting contracts, do so here. If you opt to keep them, edit each one so that it uses your desired platform preference. You want to do this before they run their first trial, as once they run their trial, they may have "any" platforms which will make life more difficult later on.

Here, I'm going to opt to delete them all, and start from scratch. I do this for three reasons, first because I often miss a contract or two, then wonder later why I have overlapping trains (those with "any" platform don't show up on the timetable schedule), secondly because I'm fussy with wanting decent contract value, and thirdly, and most critically, the starting trains on the map may not correspond to the exact same schedule as newer contracts you accept. Instead of trying to work that out, I find it just easier to delete all and start from scratch.

Deleting them is a simple case of clicking the trash icon at the far right hand side, then selecting Yes. As these are trial trains that haven't run, the Reject penalty will be 0.
Note: If you can't see the trash icon on the far right (for example, you have a bigger UI than default), look for the horizontal scrollbar, or click on a blank part of the contract area and drag to the left.

Press play to allow the contracts to start generating. When a few appear, feel free to pause again to give yourself breathing room.

For your first contract, you need to make sure that the platforms are just right, as all future contracts will take the same platform arrangement.
Being a Brit, I always change my platform arrangements to be left hand running. Most maps are pre-configured for right hand running (even on British maps), so check that the platform arrangement is how you like it.

One final change is the times of the train. For the first contract, move the time "back" to 08:00. One of the quirks of the trial trains is that you still get the tokens and money even if it comes onto the map late. Keep the other times as is - even if you think it can run quicker, leaving it as is will be easier when it comes to accepting further contracts.

For the second contract, you want to set the arrival time of the first station as 08:03 (again whether this is before or after your current game time won't matter) and leave everything else unchanged - the platforms should automatically be as you set for the 08:00 train.

You can accept any other contracts already generated, setting the third contract to 08:06, the fourth contract to 08:09, the fifth contract to 08:12 and so on. Again, don't worry if you've had to advance time to get the contracts to appear, just keep the times of the contracts in the same pattern.

Note: If you are advancing the time (either before or after) by 10 or more minutes, you can press the Ctrl key when you press the + button and the time will jump in increments of 10 minutes

Now you are ready to let the trains run. However, at this point it's all manual. So, we'll set ourselves some "goals" that we want to achieve:

• 5 green tokens, so we can get Automatic Routing
  
• 5 more green tokens, so we can get Perpetual Circuit
  
• 5 more green tokens, so we can get Auto-reverse trains
  
• 3 more green tokens, so we can get Auto-accept trains

You can do Auto-reverse trains either first or third depending on which you want automating first, routing through points or reversing the trains.

Setting trains to be every 3 minutes, we should have automation within the first cycle.

When you press play, all trains up to the current time including the 08:00 service will be patiently waiting outside the station. Some may be in "very late" red, don't panic, it's all part of the plan.
Accept the train with the longest time (the far left one). Whilst that is heading to A's platform, allocate the route to the next signal by clicking on the station signal, set the track outside B, then allocate the route from the second signal into the station.
Once the 08:00 service has cleared the platform, accept the 08:03 service, and so on until you have no trains to accept.

Once the 08:00 service has cleared the tracks between A and the approach to B, accept the 08:03 onto the tracks.
Reverse the 08:00 train, if the train is still approaching the station the locomotives will turn yellow to indicate they will reverse once they reach B), or do so when the train is stationary in the platform if you feel more comfortable with that. When the 08:00 train arrives at B, set the points and signals back to A.
Here, we have the 08:00 service at B, and we've routed it back to A. The 08:03 service is on it's way to B, with yellow locomotives to indicate it will reverse when it gets to B. The 08:06 service is approaching B.

If you think it's getting overwhelming, just press the space bar to pause time. Really, there is no penalty for doing so! Press the spacebar and take a breath, calmly do the actions you want, then when all is done, press space bar and let time flow again.

We've accepted a few contracts and trains, and we'll just repeat that until we have a full bank of 20 contracts per cycle.

You may want to keep an eye on the contracts you've accepted, and if there's room for more. To do this, click on the station label, and a small window will appear at the station with the timetable. However, this will move when you drag the board, maybe you want it in a fixed position? To do that, just drag the window to the left (or right) of the screen, when a grey panel appears affixed to the left (or right) of the screen, dropping the box will cause it to be fixed to the top left (or top right) regardless of where you are on the map.
Note: It will default to showing just 30 minutes. Pressing the arrow to the top right of that box will expand it to show the entire hour

Now it's time to accept more contracts. One thing I like to do at this point is to set any station I am not interested in to a Red colour.
In this example, the contract wants to go to NY Penn, but I am only interested in my two starting stations. What I do at this point is either middle click the station labels I don't want to serve and change them to red, or click the contract so that it shows where the station I'm not interest in is, middle click on the station label, select the red station colour, then right click to come out of the setting screen. Now when I hover over a contract with that station, it will show red, and I can instantly reject it without spending any time thinking about it.
Remember, you can change the colour any time you want. Changing your strategy to another set of stations? Great, you can change the old ones to red and the new ones to your desired colours.

Now the trains are moving, we can get into a rhythm of rinse and repeat.

Once every three minutes, you'll:
• Accept the train into Station A
  
• Clear signal at Station A for route towards Station B
  
• Set points and clear signal into Station B
  
• Set the incoming train to reverse at the station
  
• Set points and clear signal from Station B
  
• Clear signal into Station A
  
• Accept the contract

Tip: You don't have to wait for the train to clear the section (don't do this in real life!), if you know the train is clearing the section, you can accept the next train straight away.
Here, the signal was cleared into Station A whilst the previous train was still moving towards the sink. The track shows white, but the next train will still run okay. The same happened in the other direction, since the train at Station B had a clear route to the station, I set the signal for the train at Station A to continue.

One thing that is obvious when you do repetitive things, is that it is, well, repetitive. Great for the first few times, but not so after doing it lots of times. Let's fix this by getting automation to start doing some of those steps.

Once the 08:12 service has left the map at 08:23 (or a little after that if your trains are still running late) you should have in your bank a wad of cash and 5 green tokens.

With the 5 tokens, you want to get your first automation. I'd suggest Automatic Routing which will save us having to click the points twice every 3 game minutes.
Continue with routing the trains until the 08:30 has run through the map, and you have another 5 green tokens. You may (will) get alerts to say you have reached Tier 1 Red and Tier 2 Green, but don't worry about those just yet, let's continue with our 20-green per cycle plan.

With the 5 green tokens, we want to research Perpetual Circuit. With that under our belt, we can now automate a chunk of the work. Before setting the next train from Station A, let's:

• Upgrade the signal on Station A's departure platform to an automatic signal, and add a perpetual circuit to it
  
• Add a new automatic signal about half way down the track, and add a perpetual circuit to it
  
• Add a perpetual circuit to our automatic signal near Station B
  
• Set the track from Station A to the half way mark, and from the half way mark to Station B's approach signal to perpetually repeat

To set the perpetual circuit, click the signal, then press and hold the SHIFT key whilst clicking on the track to set.
Note: Running out of money? Just sell some Conductor Offices until you have enough cash.

Once a train arrives in Station B, repeat on the other track:

• Add a perpetual circut to Station B's automatic signal
  
• Add a new automatic signal about half way down the track, and add a perpetual circuit to it
  
• Upgrade the signal outside Station A to an automatic signal, and add a perpetual circuit to it
  
• Set the track from Station B to the first automatic signal, and again from the first signal to the second signal.

You can't yet set a route if there's a train already on the section, so you may need to wait for a previous train to clear a section before you engage the perpetual circuit.

Wait until the train in Station B has left the station, then engage the perpetual circuit from the approach signal into the station. If you haven't already done so, when the train arrives into the platform set the perpetual circuit from the station back towards station A.
With both signals having a solid white ∞ infinity symbol, the track will automatically route into the platform for a train, and as soon as that train gets to the station, it will route it out of the station.

Double check that all of the signals are now Automatic Signals with white ∞ infinity symbol. With this, you now only need to reverse trains and accept new trains.

As soon as you get 5 more green tokens, research Auto-reverse trains so that you no longer need to worry about reversing the trains, and 3 further green tokens, research Auto-accept trains.

When the 08:51 train leaves the map, you should have the required green research to have all four main components of automation, and at this point the map should now be able to run unattended - it should be automatically accepting the train, pathing the train from Station A to Station B, turning around, and pathing from Station B to Station A. This should equate to 20 green tokens an hour and your first gold star!
Our trains may be running, but we're not getting paid well for them. This is because they're at 40km/h and the full money's at 120km/h. First, let's learn Basic Tracks, a Tier-2 research requiring 10 green tokens. Now, upgrade all your tracks (press C over each segment in build mode). You'll immediately notice the trains running quicker, but then wait outside the stations for the platform to be clear. So at this point, we'll want to update the train times. But commuter trains can run at 120km/h, whereas Basic Tracks only upgrade tracks from 40km/h to 80km/h. You may want to save up another 35 green tokens to get the Advanced tracks - just set the speed to 25x and wait until around 11:30 game time. With enough tokens, learn Advanced tracks, and repeat the upgrade so that all tracks are 120 km/h.

Note: Money might be tight, depending on how profitable your contracts were to this point. You may want to shave some Conductor Offices, or leave the map run for a couple hours until you get the required finances.

With the tracks upgraded, it's time to fix our schedule a little. You've probably accepted any contracts up to now, including those really uneconomical 1,000 contracts which won't bring much money even if we get full contract value, so look for the lowest paying contract you have, and dump it. To do this, open the contracts view (press I) then click the little arrows next to "Reward/Max" so that it sorts in order, then trash-can the cheapest one
Your previously nice looking schedule now has a ghastly hole in it. Sacré bleu, that won't do. Let's fix it.
First, we need research that allows us to change the timetable. In Tier-1 Green learn Timetable Adjustments for 5 green tokens. Close the research menu.

Next, we need to know what timetable we should have for full pay. Click on a new contract, and check the timings we need for the trains. Set the Arrival time at the top station A to xx:00 and then note the times for Station B and return time at Station A. This will be your new times. Cancel the new contract window (right click on a blank bit of screen, or press the X button on the contract dialog)
Look at the schedule for that glaring hole in the timetable. Click on the first incoming train after that gap (the panel at the bottom will show the train's details when you click on it) then press X or select the button "Contract Configuration for schedule editing".
With the Active Contract window showing, adjust the Arrival times of the second and third arrival times to match what you calculated above - in this example, the second arrival time will always be 3 minutes later than the first arrival time, and the third arrival time will be 3 minutes after the second arrival time. There may be yellow overlap warnings on the second and third station, this is to be expected at this point.
Click on next train (to the right of the yellow time bar) and repeat, press X or select the button "Contract Configuration for schedule editing", and adjust the times of the second and third station.
Repeat this for about half your contracts. You may find it easier to look for the gap in the second station's panel to know which train to click on next.
Let your trains run for a bit, until it gets to that transition point (between the old timetable and the new timetable) - the first one or two trains may be late and not get you your green token/payment, but this is just for the one cycle. You should then find there's less trains on the board at the same time, probably one train in Station A departure, one in Station B and one in Station A arrival.
You may also have noticed two gaps in the timetable. One is the transition between your new timetable and old timetable (we only did half the contracts earlier), and the second is the transition from old timetable to new timetable on the next cycle. Click on the train to the right of the first gap (the first old-timetable train you need to change) and repeat the earlier update process (press X or select the button "Contract Configuration for schedule editing", and adjust the times of the second and third station)
All that's left is to accept another contract to fill in the gap we made earlier. Remember to change the time so that it fills snuggly into the timetable.

So, the final step is to make it an intensive service, operating at 30 trains an hour. The main inconvenience with this is that the game can make quite a bit of noise every two game minutes as it alerts to you an incoming train. If this bothers you, but you want the rest of the sound effects, press ESC to bring up the options, select Audio, then move the Alerts volume slider down then close the menu.
We're going to need more contracts, so if you haven't already done so, you may want to research More Contract Offers in Tier-2 green so that you get additional contracts to choose from.

What we're going to do is run a train every 2 minutes, so we'll adjust the timetable of all the odd-numbers of arrival time in the first station. To do this, hover over the times of the trains on the schedule after the white current time, and find a train with an odd number of minutes.
As before, we want to edit the contract, so press X or select the button "Contract Configuration for schedule editing". Bring the arrival time down one minute (this will cause a yellow overlap on the timetable, this is to be expected). The next train will be even, so skip that, then pick the odd train and repeat. You'll see a pattern emerge, two yellows followed by a gap.
Repeat this for half the contracts. Why only half the contracts again? If you inadvertently pick the next cycle's train to edit, it can revert to the current-time contracts and cause you to get a little muddled, so best to do half the contracts, let it run for a few minutes, then finish the rest off.

After you've done all 20 contracts, your schedule should now have yellow and blanks throughout (the right most will show blue every other minute, this is as expected)
We now need to fill the blanks. Locate a blank spot in the schedule, and hover over the train before it, and note the time, then hover over the train after it and note the time. We want the time exactly half way between (which will be an even number).
Here we have a train at 14:38 and 14:42, so exactly half way will be 14:40. Accept a contract with that arrival time. You know it's done right if you have five yellow blobs uniformly in a row, followed by a gap, then two yellow blobs and so on.
Repeat adding 4 minutes for each new contract, so in this case, we'd add one at 14:44, 14:48, 14:52 and so on. Again, only do about half of the contracts, let the map play for a little bit, then finish up the rest of the contracts. If you lose your place, just go back to the previous paragraph of checking the train before and after the gap, and working out the time of your new contract.

If you get any "Delay Risk" trains, you might have made a mistake, so feel free to reject that contract and redo it.
Once you've filled all the gaps, you should be left with 30 trains an hour, operating every 2 minutes, with full pay and green tokens.

Can we get more intensive than 30 commuter trains an hour with two sinks? Well, yes. We can get 60 intercity trains an hour from two sinks. This needs a little more work to achieve, so let's get stuck in.

First, we need to research Intercity which is located in Tier-2 Green. You will also need Arrival Sensors, Departure Sensors and Routing Queue. Not essential, but you may also want Tier 3's Structural Contracts Manager, Faster Switches and Corridor Tracks. This is a lot of Green Tokens, so you may need to run your intensive service for quite a few cycles to get the required tokens.

With the Structural Contracts Manager researched, open up the Automated Contracts Manager (press C) and take the tick out of Commuter, so that you are left with just Intercity contracts being generated.
Some maps may let you create an A>C non-stop intercity route, if your map has these, then by all means set up a train every 1 minute between them, and you will have achieved the goal. However, most maps don't have that contract availability, so we will look at the alternative A>B>C where the train has to stop at B. This is available on all maps with Intercity trains.

For the contracts to work, we need a sink at A and a sink at C, both accepting Intercity trains, and an in-map station at B with 3 platforms (6 if you want to run the trains both ways) where the station also accepts Intercity trains.
Pick one of the sinks that has lots of space for Conductors Offices and build a few offices.

Connect the line between A and C (leave out the area near the Station B for now, we'll come to that in a minute). Full blown IC tracks may cost over a million, so either wait for your intensive commuter services to rake in the money, or use the fastest you can afford. This still works (although not returning full money on the contracts) if you use slower tracks.

For the tracks between the two sinks, provide auto signals fitted with perpetual circuits near the mouth of all auto-route blocks, and no more than 1km between signals on open stretches. Shift-click the track to get the length, if it's more than 1000m, put another signal between the two. This helps prevent the trains slowing down when travelling across the map. Engage the perpetual circuits on all the tracks.

For the station, we need three platforms (for each direction if you are doing both ways). The approach track needs an arrival sensor that is 500 or more km from the auto signal (place them inside an autoroute if the autoroute is close to the station). Each platform requires a departure sensor and an Auto signal. All other tracks should be set to perpetual routes.
Set the arrival sensor to control the Auto signal just before the platforms and route it to the station.
Set each departure sensor to "Other" for the desired exit track. If you opt for the station names for direction, be aware that the intercity train may be looking for a passing station rather than the sink station.
We are now ready to accept contracts. Pick an A>B>C contract, and set the platforms. You'll have three platforms at the in-map station B, so pick one (I typically pick the left/top most as it's easier to visualise) and set the time to be divisible by 3 (so xx:00, xx:03, xx:06, xx:09, xx:12, xx:15 and so on). Watch the train by pressing T, and make sure it goes through the map as you expect. This is handy in case you've done C>B>A in error and haven't yet set that route.

All going well, accept a second contract, again set the time divisible by 3 (not the same as the previous train) and again watch the train by pressing T. Make sure that all the perpetual routes behave as expected, and the train routes correctly through the in-sink station. If something goes wrong, fix it, and when you accept the next contract, watch it again, until the train makes a flawless route requiring no intervention.

Now accept another contract, again following the divisible by 3 pattern (obviously not taking the slots you've already got a contract on) until you have 20 contracts.
Now we want to get the next platform at the stopping station filled, and to do this, we need to set the trains one minute later than those we've already created. Set the time to be one minute after an existing train. If you set it over an existing train, the scheduler will show a yellow, which is bad. Move it up one minute until it is blue. You will also need to change the platform of the stopping station. Again, press T to follow the train. Make sure it goes through the map as expected, particularly around the station stop.

If all went well, repeat with another 19 contracts.
You can now repeat with the third platform, so again create it in the minute's gap (xx:02, xx:05 and so on) and change the stopping platform to the third one, and watch it again by pressing T and making sure it does the journey as expected. If all goes well, repeat with another 19 contracts, and you should then be left with a service every one minute.
You can repeat this in the other direction, going C>B>A too, an intensive 120 trains a cycle!