The autodesigner, frankly, is not very good. It's probably best if you design your own ships.
Also, special techs like the Terran warp bubbles...I forget the proper name!....in another thread I read that you should just put them on one of your ships in a fleet and not all of them, but I don't really understand that. Doesn't the tech just automatically upgrade all the ships you have once you've researched it?
I'm not quite sure if I understand this question, but multiple fleet modules in the same fleet, IIRC, do not stack, so having multiple ships with them in the same fleet is redundant.