Some races have better base ships then others so this may not apply to all.. Still, it doesn't hurt to make sure and it definitely helps the humans. So click the shipyard button.

Redesign your 'scout' - 2 small reactors, a cockpit, 1 small warp and 1 'small engine'. fill up the rest with power conduits and set it to avoid combat. Its costs less then the default scouts, and is almost 4x faster. It will outperforms 2 or 3 normal 'scouts'. Set it to avoid combat and save it with a new name. Opteris scouts are a little larger resulting in the requirement of 1 fuel cell. Kulrathi modules need creative placement such as in this image to operate.

Transports - Make sure it has 2 warp engines, 2 small engines, a cockpit, a medium reactor. Cram the rest full of cargo holds and make it avoid combat. This new transport is about 3 times faster and holds more cargo.

Colony ship - 2 warp engines, 2 small engines, a cockpit, a medium reactor, a colony module*, and fill the rest with power conduits. As usual, set to avoid combat. Before you ask, small cargo holds wont increase your colonies starting food/production so there is no reason to include them.

*Extra colony modules will give +2 food/prod, but you need large freighters before you can stick enough on to start a colony off with a rover bay.

Now that your designs done right-click your scout and have it refit to your new fast scout. If your side doesn't start off with a prototype flagship you start with 2 scouts.. so refit that one to a fast scout as well. You should still be paused, so nothing will move yet.

Lastly, you need to make sure your auto colonize and freighter options are set to use your new optimized units each game unless you micromanage it yourself. If you want the AI to handle your food management be sure to click the AI button and change things around

Go to the research screen (it says 'Choose' in the upper left hand part of your GUI). Make sure two+ things are qued up just in case you get in combat and dont notice a completed research right away. If you have a plan of what to follow go for it, otherwise a few suggestions in no particular order are...

-Industrial foundations to boost colony production (One of the best first technologies to research)
-Xeno linguistics for fast non-aggression pacts with ai (this wont stop them from declaring war on you if your military is weak)
-Interstellar governance for quick cash (if you are fielding a huge fleet)
-Military outposts are for rushing/anti rushing troops on colonies (works best after researching Industrial foundations)
-Aeroponics to make low food words more sustainable so your empire can grow faster.
-Missile theory better fighters (especially if you took the Blind Trait)
*personaly I choose missile theory, and then industrial foundations

An important thing to remember: Raising your tax rate will slow down your research rate.

Now its time to exit out to the star map and decide if you want to be Social or a Space Hermit.
-If you want to be social, Go to your colony screen and que up another fast scout.
-Unpause and wait for your 1-2 slow scouts to enter the build queue for refit and pause again.
-Que up 3-4 Soldiers (good for defense, as well as exploring anomalies. Maybe queue more if on brutal difficulty)
-Que up a bunch of attack ships (you may want to design these yourself)

If you plan to be social, you will want to tell your scouts to 'explore' as soon as they finish building.
If you are a Space Hermit you will probably want to explore a few systems manually and then go hide in your home system before you meet anyone.

And there you have it! Be sure you unpaused and go out to do Space Stuff.

-Buy a spy or two and train them up a bit.
-Refit your colony ship to your fast colony ship design.
-Send out 30 or so 'fighters' to a planet guarded by the remnant and kick their butts. Then colonize whatever they were guarding.
-Pick a fight with an AI, swarm them with combat ships and land troops on their planet.