As in a lot of things, it depends...
Personally, I go for two quick civic labs, and then don't go back to that screen for a long time. I tend to grab as many early planets as possible and need to be able to coonize anything I find. With two, you can buff your resource gathering, colonize Ice/Volcanic, and get trade ports. Thats enough for a damn good start. Later on three more will get you into Econ-boom territory, but thats a late game scenario.
Then I move on to the military tree. By this time your scouts SHOULD have a good map of the system. You can tell who you're facing, and where they are. Are they close ? It's LRM's. Far ? Kodiaks and Carriers. Weapon tech's are nice, but they don't work for all your ships : Laser upgrades are useless for Kodiaks, carriers, and LRM's. Cannon upgrades don't help Carriers, LRM's or cobalts. Missiles don't help kodiaks, cobalts, or fighters... But Armor, Hull, and shield upgrades help EVERYONE. Drop your first upgrades here and you won't go wrong. It only takes one military lab to get rolling and at this level they are cheap. You want both armor and hull, and as long as you have 6-10 LRM's/cobalts and a cap, then the first tier upgrades will give you a slight edge.
Aftet that, it's purely situational/personal. With Carriers, I prefer to work the missile tree and go exclusively bombers, keeping flaks ( lots and lots of them ) for cover. This works well with LRM swarms, since both get the buff. My typical Lrong Range fleet has 10-15 carriers, 20 Flak, 20 LRM's, and a level 6 Marza to keep the enemy from getting to close. The extra 20-30 percent damage adds up. Ging Kodiaks ? Work the cannon tree. It's rare that you find yourself with enough cash to work multiple trees so specialization is going to happen, to a degree.