Offic3rHotpants: The AI always uses the universal warehouse. So if you've turned that off then you're only handicapping yourself, for starters.
blodfox112: How about city spamming? do you just spam out stuff like resource gathering cities (farms wells etc) and factories/forts for extra income?:3 How about techs? I understand the archive is a pseudo tech tree but it still confuses me a tad!
I'm not an expert at the game in spite of all my years playing it and I'm a turtler when playing strategy games, so bear those in mind. I like to lock down my current location first and then move on. In EFS that takes the form of exterminating the local resistance on my homeworld, getting a solid infrastructure in place and then repeating on a neighbor.
So what I do is I build a few farms, mines and wells to get a steady supply of primary resources (food, metal, etc) flowing. Next is to get three militia and a pair of anti-air and artillery in all my new or understaffed cities for defense against rebels. Then I build a few factories for simple tank (and occasionally ship) production. Once I've got two or three stacks of basic tanks (usually 4 med, 2 each of artillery and anti-air), I subdue my homeworld. Capture every city, plunder every ruin. Don't forget to use your cruiser to soften more powerful rebel stacks during this period (back out of an attack on a ruin if it's full of tanks and hit it with the cruiser first, for example). After that I start pumping out engineers for more primary resources, secondary resources (electronics & chems) and one or two labs. Try to place your labs so that they're surrounded on all sides to protect them from trouble down the line, and remember that labs are expensive (so don't crank out 20 of them at the start).
Forts, in my experience, aren't as useful early on. They're only really good for officers until you have some solid infantry tech. The basic infantry you can unlock for them near the beginning aren't really any better than militia unless you build a massive stack of them. Officers will slow down your tank stacks if they're moved with them but their bonuses are useful. What I do, then, is build one or two of them and then use landers to add them to the tank stacks when they're adjacent to the enemy. In this way you can ship the same officer around between multiple fronts as needed.
With regard to resource production cities, for the early game it's sufficient to just have 2-3 each of chem & electronics cities, adjusting as your needs demand. Just monitor your trace & energy harvesting to make sure you don't exceed them. Once you have access to arboriums food production gets easier and you can afford to feed more cities. You may consider taking a "green" world if you're playing as house Li-Halan since they start on a desert planet. Later on, when you're producing tertiary resources like ceramsteel and singularities, remember that the rule is that one city can supply one city. One electronics city (after it's had a few turns to reach full health and thus full production) will supply one fusorium, for example. I'd advise focusing most heavily on ceramsteel and, to a lesser extent, monopols once you reach that stage. Biochems and wetware, while useful, aren't used as widely (and wetware is expensive as hell to produce, requiring four supporting cities plus a lot of food, energy and trace to supply them all). Singularities are only used for interstellar craft so you can go for a while without worrying about those as long as you take care of the ships you start with. Just remember to pull your freighter from Byzantium II to your homeworld and to avoid landing on open terrain with your non-lander ships unless it's important to get a mass of units into place fast (though they can handle one or two landings fine as long as you station them in a city to heal afterwards). When you start moving to other worlds, try to avoid landing within about 6 hexes of large clusters of cities as there will almost always be PTS units stationed in them who'll take shots at your ships as they descend.
As for technology, the archive is, indeed, your tech tree. Jump to the end of a given entry and it'll tell you which currently available technologies you'll need to research to reach it. Just be advised that a lot of tech--particularly unit tech--comes at the end of a LONG web of research, and several of the links in the web will be proscribed (red). Don't go researching proscribed techs unless you're confident that you can defend your labs (and world).
On a side note, NEVER trade a map of your homeworld to anyone. If you've researched proscribed tech in a lab on that map, and that map gets into the hands of the church, they'll know. On the other hand, you can give maps showing the locations of other houses' labs to the church to potentially sic the inquisition on them.
And as a final note, don't be afraid to set the AI to a harder difficulty than yourself. If you leave them on beginner, they'll get a bunch of advantages in addition to whatever "corrective measures" they're given under-the-hood to bolster their strength (like free units).