With #1, that is the intended behavior -- the manufactories manage themselves by default, and there's no reason to turn on if you have a huge amount of resources of what they would produce; that's just being wasteful of your overall resource income. There is a control node that you can build that will let you manage them completely manually, though, if you wish. But in general, there's not much of a reason to do so.
For #2, that must be a factor of the type of AI you are facing off against; one of the more defensive ones, perhaps a Turtle of some sort or something along those lines. I don't remember exactly which AI type does that, but there are definitely some that do. On the plus side, you're going to have an easier time defensively, generally, with an AI type that is itself defensive.
Generally speaking, my advice when facing an AI that is doing something like that would be to take the fight to your own territory. If you're a big user of starships, that's really the only way you'd be able to maintain your preferred ship mix. If you normally use smaller fleet ships (as I tend to), then just focusing more on the mkIII/IV unlocks would let you fight in their territory, but still you'd take more attrition than you'd probably want.
Basically, the idea of taking the fight to your own territory is that you should fortify yourself heavily with turrets, ships of the sort that would get killed in their area, and so forth. Then sweep in with a wave of cloaked ships, or bombers, or something else fast and at least somewhat durable (and cheap, if possible) and just kill their command station. If the command station is under a force field and you don't have something that is able to pass through force fields, then that is more of a challenge, but you can still pop an EMP in there and then send your guys on a raid. You can also use transports either paired with the EMP tactic, or just in general, to make it easier to do a quick raid on their command station.
Anyway, once you've destroyed the command station, then you're back to the mode where your riot starships, etc, are useful again: cross-planet defense. The AI will swarm you with all its stocked ships, of course, and if you've got sufficient defenses (and preferably some bottlenecks for them), then you can pick them off quite well. This sort of tactic often works wonders in general, because it's a way to fight away from all those nasty turrets that the AI tends to hide inside.
The downside, of course, is that then the AI is the one "setting the tempo" on their attack, and if your defenses turn out not to be sufficient you've probably just lost the game. And, instead of being able to pick them off one guard post at a time, you're left to face most all of them at once (at least sans turrets).
If the AI is massing at a wormhole with so many guys that you'll never be able to defend against them, consider sending a lightning warhead or two through. That also can make a big difference with CPAs, incidentally.
In short, that sort of strategy is not without risk, but when compared with the inevitable slog you're otherwise facing, it seems like the clear winner to me. And hey -- with each planet you use that strategy with, you can actually avoid killing any of those big defensive things, and can instead capture them for your own use. That would then make future such defenses even easier if you've got an ion cannon and orbital mass driver on your side (core warhead interceptors are useless for you since the AI doesn't have warheads).
Good luck!
(P.S. -- This turned into a strategy discussion, so I'm moving this to the strategy discussion forum)