A few quick tips for new players:

- The starter engine (Octergol) is already obsolete when the game starts. Insta-researching a better one should be a priority. Cooling M is also useful right away. The Water Tank M is another good one. The Compressed Fuel Tank is extremely useful, but it can be fun to try and make the regular tanks work and researching fuel tanks normally.

Engines of note:
- The NP-27 is much shorter, 40% faster, requires less energy and cooling, and requires 3 technicians. Probably the cheapest you should consider.
- The Bussard is the fastest of the solar (first tier) engines.
- Since the Bussard is the fastest, you might be inclined to ignore the Orion Engine, but note that it only requires 2 technicians. That makes it worth considering when using CyO's, or when one person makes all the difference with the stored air/water.
- The Fission Forward Engine is the only interstellar engine that will fit easily in the Bug. I used to think it was the only one that was possible, but someone proved me wrong. :)

- For ships that you own, more speed allows them to complete their tasks faster, which in turn allows you to earn money faster. Thus, it's generally worthwhile to spend more making your own ships more "uber" than what you might typically sell. The food and ore transport missions, in particular, come to mind here. For missions where the customer is buying the ship, cost is the primary factor.

- When you set a budget for a research category, note the color of the number text. It isn't explained anywhere and it took me ages to figure it out, but if the numbers are red, then you're spending more money than your researchers can use, and it will just get wasted. I'm not clear on whether yellow means partial wastage or not. $2250 seems to be the highest that remains in the green.

- Budgeted research is not divided between each item, but rather applied in full to each. That means that if you budget 2000, then each item progresses by 2000. One would naturally think the number gets divided by the number of projects, but nope.

- You can only assign one of your ships to a service contract if it's inside the blue circle of the system the contract originates at. If your ship is outside of the circle, you need to bring it over before you can start the contract.

- When looking at the required specifications for a mission, almost all of the room requirements are "at least", meaning that using a more advanced version is permitted. Using the Advanced Cannon when it lists the Basic Cannon, for example.

- When using the right click radial menu, just release the mouse over the desired option e.g. Suit up. I kept left-clicking, but this only cancels the menu.

- Typical RTS control groups work. Use Ctrl+number / Shift+number to select. When everyone is overlapping, it gets really hard to select people, so this really helps with that.

- In the Ship Designer, press Z to undo your last action.

- For the Standard Operation crew mission, when creating patrol routes, always set at least 1 second on a waypoint to make sure it resets the timer properly.

- Some rooms need pilots or medics to perform maintenance, rather than technicians. Make a note of these and try to place them near each other, along with the appropriate living quarters.

Pilots
+ Bridge
+ Computer
+ Small Armory (only)
+ Sensors
+ Communication
+ Navigation

Medics
+ Water Treatment
+ Sickbay
+ Galley

To repair hull breaches:

1) Turn off the power to the room with the hull breach *and* the room or corridor next to it. This turns off the life support to those rooms, and thus the air pressure.
2) Put a technician in the room next to the room with the hull breach, and lock the hatch behind them.
3) Now open the hatch to the room with the hull breach. Give it a second for the air to finish venting into space.
4) Both rooms are now at vaccum. As a result, the technician can now approach the hull breach without getting sucked into space.
5) Repair the breach.
6) Turn the power back on.
7) Move the technician away in case the room gets hit again.

Brown = Worthless asteroids or other space debris.
Red = Area of pirate activity or other hostilities.
Yellow = Valuable asteroids that can be mined.

Encounters

When a ship encounters an asteroid field, a popup asks if you want to stop or proceed through it. I've never had a ship fail, but I'm guessing that the chances of success are affected by either the ship's rating for the Asteroid Field mission specifically, or its ERS rating in general.

When a ship encounters hostiles, a popup asks if you want to attack or retreat. High engine speed seems to help with the chance to succeed at retreating. It certainly reduces the number of times retreating is necessary, since the popup can appear multiple times while travelling through a red area. The chances of success when attacking seem to be determined by either the ship's two Ship Battle ratings, or its general HEP rating. However, the option to attack will always have impossible odds if the ship doesn't have any weapons.

Contracts

Contracts are divided into two types:

- Purchase contracts are shown with a circle icon, and with these contracts, the ship is delivered to the customer instantly when construction is finished.

- Service contracts have a triangle icon, and with these contracts, the ship is added to your fleet when construction is finished. They're basically a filter for the "Build your own ship" option. When selecting one of these contracts, the list is split into two sections. The top of the list displays all of the ships you already own. The ones in green are both capable of performing the mission and available for assignment. A ship must be within the blue circle of the system where the mission originates before it can be assigned. The bottom part of the list displays all of your ship designs. The ones in green here would be capable of performing the mission, once built.

- Campaign contracts all have a service triangle icon on the list, but they are shown in blue. Contracts that ask for X number of ships will first add the ship to your fleet. When each ship is built, it must be assigned to that contract mission, which is to fly it to a blue delivery circle on the map. Be sure to assign the ship to the mission first, or it won't work.

You really only get a feel for good room positioning when playing the crew missions manually. There are groups of rooms that should always be placed near each other. Also certain layouts are much easier to defend than others. For the most part, auto-resolve doesn't care about room positioning. The one exception is it does seem to loosely care about it for the Standard Operation mission.

Some of the missions are somewhat borked, or just impossibly difficult. The Ship Battle missions, for example, are insane. All of the ERS missions except maybe the CyO Malfunction mission seem to be interesting and work well, in my experience.

For the HEP missions, if I have an armory I always make an attempt at manually playing the Probe Drone Attack and Anti-Piracy I missions. Success is far from guaranteed, but when you can pull off Anti-Piracy I with just a group of crew armed with pistols, it's very satisfying. It's certainly easier if you have some security guards with assault rifles. However, be aware that the number of enemies does scale with bigger ships and/or more crew members.

- Note that in addition to the Auto-Resolve All button at the top, there are auto-resolve options for just the SOP, ERS, or HEP, as well as an auto-resolve for just the currently selected mission in the bottom right. This allows players to pick and choose what to auto-resolve and what to play manually as they see fit.

- If you auto-resolve the Yellow Alert and/or Red Alert missions, then the crew will always start in their quarters, without a suit on, and unarmed. Playing the Yellow Alert mission manually, for example, allows you to order them to put their suits on, then go to their stations, and start from there when playing any of the yellow missions. You can optionally have all or just some of them grab ammo before going to their stations during the Yellow Alert mission. This will lower your score in the Yellow Alert mission, but might be worth it if it improves your ERS score.

- Always make use of the pause ability (P) when giving orders.

- If you can manage to place a sickbay at a choke point, with the armory directly behind it or next to it, with the bridge, computer, life support, at least one generator, and no hull entrances behind it, then you can have all of your crew make a stand in the sickbay. It's not always possible or worth the effort to set things up this way, but sometimes it can make a big difference when playing the missions.

- Note that there is a Mining Operation SOP mission below the Blue Alert mission, in case you missed it.

Here are some tips related to specific crew missions, when played manually. Auto-resolve doesn't care.

Major Collisions and Asteroid Field (also Minefield, to a lesser extent):
When designing ships, try to leave some empty space at the front of the ship. While empty hull squares don't have nearly as many hit points as armor plates, they still add more hit points that need to be smashed through before the ship starts losing rooms. Likewise, armor should be added to the front of the ship first, and to any bits that stick out from the sides. Wide ships have a much harder time with these missions.

Besides that, avoid putting the most critical rooms at the front, such as the bridge, life support, the main (or only) power generator, or the only air tank. Crew quarters are ok, just remember to move the crew further back when the mission starts.

Firestorm:
Space suits not only provide crew with air to breathe, but also provide some protection against fires (and firearms). So, everyone should have their suits on for this one. If you put them in suits for the Yellow Alert mission, then they'll automatically start with suits on. Different crew types are more or less effective at fighting fires. They are, in order from worst to best: Medic, Pilot, Technician, Military, and CyO.

Power Failure:
For this mission, all of the generators have failed simultaneously. This means the ship's computer is down, and all of the rooms are dark, which greatly reduces crew movement speed. Make a note of the minimum number of technicians required to work on each generator, and divide your technicians up to bring all of the generators back up as quickly as possible. Watch a generator's power button while it's being repaired. It will start out flickering rapidly. As it is repaired, it won't flicker as fast. Once it gets up to 50%, the flickering will stop, and you can switch it on. The mission ends once all of the generators are running.

• If you can get enough power to turn the lights back on early in the mission, the technicians will be able to reach the rest of the generators much more quickly.
  
• Note that generators labeled as "Emergency" generators do not go down in this mission. They start out running and at 100% when the mission starts. Having just one could keep the lights on and make getting to the regular generators much faster. If all of the generators on the ship are emergency generators, then the mission immediately ends with maximum score.

Alien Infestation:
This mission can be impossible in a lot of situations, but there are ways to get the maximum score.

• Firstly, immediately pause and lock any hatches connected to the engine room. Turn off the power to the cooling rooms. This will raise the temperature in the engine room, which slows down the reproduction rate of the bugs. This will also lead to fires in the ship's computer, but usually that can't be helped. On a large ship you might provide cooling to the computer on a separate circuit.
  
• The bugs eat metal. They will eat through hatches, through the walls between rooms, and through the hull to the exterior. Vacuum does not affect them, and they reproduce exponentially faster in cold temperatures. Also, they randomly take bites out of the suits of nearby crew, although they do not actively target them.
  
• If at any time, the bugs eat through the hull and create a hull breach, the ship is doomed. A hull breach will prevent the temperature from rising due to the cooling rooms being off, and greatly accelerate their reproduction. In addition, they can exit through the hull breach to the exterior, where you cannot reach them. From there they can eat their way into anywhere. There's no way to save the ship once this happens.
  
• The first nest always spawns in an engine room, but the location within the engine room is random each time. If the nest spawns all the way in the back of the engine room, right up against the exterior wall, you may want to just restart.
  
• During ship design, you can give yourself a little more time by having some empty space between the engine room and the exterior hull. An extra square on each side that faces an exterior wall can help a lot. Likewise, adding armor around the engine room will also buy more time. If you haven't cleared them out by then, you're most likely doomed.

1) The easiest way to do this mission is to arm your crew during the Yellow Alert mission. Then you'll have armed technicians in the engine room the moment the mission starts. Pause, move them near the alien nest, and order everyone else to get over there to help. Move them to just outside the hatch, then unlock it to let them through when they get there. Order the medic(s) to stand near the nest and disinfect. Usually this will result in an easy win, but sometimes the disinfect doesn't seem to work properly and I have to try again. With this method, it's usually over before any fires start.
2) On ships without an armory, the odds aren't good. Your only hope in this situation is the heat buildup from the cooling rooms being off. Your medic will have to try to disinfect without anyone providing cover fire.

Tech Drill:
At the start of the mission, the condition of all of the rooms in the ship are at critically low levels. System failures occur randomly throughout the ship. Send technicians out to deal with system failures as they happen, and try to repair rooms up to at least 50% in between time. Rooms at or above 50% won't generate system failures. If a system failure is left unresolved for a long time, it can lead to power outages and fires, greatly increasing the gravity of the situation. Spread your technicians around and pause whenever a warning pops up. If you stay on top of it, you will never get a fire. This mission is time based, so you have to keep going until the timer runs out.

Medical Emergency:
A very simple mission. Get the injured people to the sickbay. Get the medic(s) to sickbay and assign them to heal. Wait for everyone to heal up. Done. If the ship doesn't have a sickbay, this mission is an automatic failure.

Magnetic Storm:
In this mission, lightning strikes cause random system failures throughout the ship. It's somewhat similar to the Tech Drill mission. Spread your technicians around the ship and respond to incidents as they occur.

CyO Malfunction:
All of your cybernetic officers have malfunctioned simultaneously and in the same way (it couldn't just be one?). They will try to reach the computer and take control of the ship, at which point, the mission is a failure. If the ship only has a human crew, this mission is an automatic zero.

• Currently this mission is very easy. When the mission starts, immediately pause and then hold down the left mouse button over a hatch, then select the option to lock all hatches. In a previous build, they were able to cut through hatches.
  
• If the ship has Corridor Turrets between the CyO quarters and the bridge + computer to stop them all, you can save time by letting them out so the turrets can kill them.

When pirates come knocking, does your crew have a plan? Most of these missions are about trying to use ship design to your advantage when being boarded by hostile forces.

• Boarding ships will always target external hatches first. If a ship doesn't have enough external hatches for the number of boarding ships, then they will cut through the hull. However, this takes them more time.
  
• On larger ships, you can do things like open the exit hatch and vent the air from everywhere except the bridge. If it takes long enough for them to get there, their suits will run out of air. On small ships, they will reach the bridge before that happens.
  
• Crew member health and suit hit points vary by type. In order from weakest to strongest, they are: Medics, Pilots, Technicians, Military, and CyO, with each model of CyO being much stronger than the one before. Note that all CyO models except the lowest can repair in their quarters. The lowest model cannot be repaired. Only military crew can use assault rifles and grenades.

Probe Drone Attack:
Unarmed drones board the ship and start mapping it, seeking the bridge. With an armory, the crew can repel them with ease, but without it, all they can do is lock all the hatches. Usually that isn't enough, as probe drones can cut through hatches quickly. Cutting through hatches uses up some of a drone's power, but there are so many of them that it doesn't really matter. Corridor turrets protecting the only route to the bridge will work too.

• Note that if a ship has corridor turrets, but no armory, the auto-resolve doesn't work properly. Play the mission manually on max speed to get around this.

Anti-Piracy I & II:
A group of pirates has decided to make your ship their next target. Pirates are armed with assault rifles, but they seem to do less damage per shot than the assault rifles of military crew members. Of course, the pirates outnumber you, so that's not much comfort. They board wearing suits, so they can take a few hits, and they can last for a time without atmoshere. They can cut through hatches, and, in addition, they have breaching charges that they can place on hatches. Anti-Piracy II has a larger number of pirates.

Military Boarding:
Similar to Anti-Piracy I & II, but these guys are each as strong as your own military crew. They come with grenades, and there are even more of them.

Mutiny:
In this mission, several crew members (all technicians) have sealed themselves in on the bridge. You retain control of medics, military, CyOs, and the captain, if the ship has a captain's quarters. However, the crew members on the bridge are not your objective. Your objective is to retake the bridge, computer, and life support by cutting through hatches to get to them and then using the Defend command in each room. Killing the mutineers by shutting off the life support, gunning them down, or any other way, will lower your score.

• Auto-resolve always gives this a zero for me. So, this is a definite candidate for manual resolve.

Computer Revolt:
This is a different type of mutiny. All of the humans on the ship turn on the ship's computer, which supposedly is loyal to you. They will try to make their way to the computer and shut it down, at which point the mission ends in failure. You retain control of any CyOs. If the ship only has CyOs, it automatically gets a max score.

• In previous versions, the technicians and military personnel could cut through hatches. In the current version, they cannot. So, like the CyO Malfunction mission, just lock all the hatches and wait out the timer. Shut off the life support if you want. Just auto-resolve this one.

SF (Special Forces) Attack:
Unlike the other boarding attacks, this one involves a small number of enemies who start out already on board. Supposedly they snuck on undetected at some point. These guys can capture rooms very quickly. Their weapons aren't as strong, so if you can get your crew to stand in front of the hatch to the bridge and hold them off, you might have a chance.

Minefield:
This mission is similar to the Asteroid Field mission, except the mines will home in on the ship. As such, they will sometimes come in from the sides. The mission mentions that the mines are attracted to heat and electromagnetic signatures. After many experiments, I found this means turning off all the generators, the cooling rooms, the bridge, and the computer. The engine too, but it's already off when the mission starts. Move people towards the center rear and seal all the hatches before turning off the computer, because once it's off, you won't have access to hatch controls. At this point, the mines will no longer home in, but the ones that drift into the ship will still explode. Hopefully the ship will survive until the timer runs out. The score seems fairly forgiving, in that 80% of the ship can be destroyed and still have a full 10 point score. The main source of score loss seems to be crew deaths.

• Since the power needs to be shut off, shields are of little help in this mission.
  
• With some layouts it may be possible to shut down everything except one shield and the necessary power, then turn off the generator once the shield gets destroyed, but it could be tricky.

Ship Battle: Offense and Defense, Mayhem:
If these missions are playable manually right now, I don't know how to do it. If someone knows how to win these, please let me know! Currently I auto-resolve these. I can tell you that selecting cannons or missiles and then double-clicking on the crosshair icon will turn it green, and then the crew will automatically fire the weapon every time they finish reloading it.