Alright, inside the capital ship I believe their are four things to destroy, the first thing is the auto turret control mainframe, that big computer thing in the middle of the turret room. Just plant two time bombs and your enemies Auto-turrets no longer work.
Each of the other rooms also contains a destroyable structure, the engines, and life support systems are located on the left hand and right hand doors, once you enter head for the panels on the far side of each room, if you can't find it look around for a health bar. (note: the life support system room has a bunch of little computers, don't bother destroying these, they don't give points or do anything as far as I can tell.)
Fineally the room opposite to the hanger entrence is the sheild generator, just destroy the huge glowing thing in the center of the room.
As for heroes, I refer you to this list:Linked!
It's an old thread, but I believe the information is accurate.
If your looking for more precise, informative information for the game in general I would suggest GameFAQ's
It's got good guides and FAQ's for games.