I've been wondering how to position my trade ports within my gravity well. Does it have any effect on their income? Initially I had thought that there would be a tradeoff between safety (distance from incoming phase lanes) and income (the speed with which trade ships can leave the system to carry their goods elsewhere). But the forum posts I have been reading mostly seem to think that income is only a function the number of ports and the length of the longest route. That seems a little silly to me, but OK.
More generally, what do you do about positioning your structures within a gravity well? I'm sure some of you have auto-position turned on. I tried that a little but it did not work well for me. I could detect no logic to where the computer places structures.
Typically, construction-type structures are more useful near the edge of the gravity well. This allows constructed ships to quickly move into their first phase jump, saving up to 20s in total delivery time. But almost all other buildings seem to be more effective close to the planet. That is, there is no reason to have them near the edge of the gravity well where the enemy can strike at them easily.
As for positioning of weapon structures, I have taken to two main strategies early and late game.
Early: guns go around the planet on the side most exposed to phase lanes. The computer never attacks from the back so it's fine to concentrate the guns on one side. After that, attempt to maximize overlap so alt+select+focus fire gets several guns pointing at the same enemy ship. I have found this technique to be enormously effective in the elimination of enemy light frigates. I assume any intelligent human would just put his bombardment on the back side of the planet, which means that guns would be even less effective than they already are.
Late: The bread and butter of my defensive forces late game have been hanger defenses. I will typically build five of those in edge star systems (systems exposed to phase lanes not controlled on both sides by my forces). I will staff them with 20% fighters and 80% bombers. Again, alt+sel+focus fire is my friend. The computer is very illogical and will automatically attack enemy capital ships with my bombers, where I really want them to be focusing on the weakest frigates as soon as the siege frigates have been finished off. Fighters of course should attack enemy fighters first, but they end up attacking enemy bombers, which means if I don't want my own bombers torn up, I have to micro.
I try to pack the hangar defenses in the tightest space possible as far away from incoming phase lanes as possible, then surround that area with as many guns as I can with the remaining tactical points. This way my strike craft can ravage attacking fleets as long as possible without me needing to worry about defending the hangers themselves. Once again, I focus fire with the guns when the enemy attacks my hangers. I think the strategy would be effective even against humans, because if they want to stop strike craft production they have to come around to the hangers. If they don't stop my strike craft, they won't have anything left to bomb the planet with.
I typically position all my noncombat structures on the back side of the planet, anticipating that when I get to my late game defensive tactics the guns will also protect them. I have never seen the computer go after isolated buildings even when they could avoid my guns, so I know that there's no reason to protect them because by the time the computer gets around to attacking them, I am already in serious trouble.
Anyway, those are just some thoughts. I used Google and this forum's search but didn't find much on this topic (the latter seems broken as neither "tradeport" nor "trade port" came up with any results). I'm an extreme beginner . . . only been playing about two weeks. Be gentle. 
