If you're looking for resources on Freespace in general (the game, the story, modding, etc) an excellent place to start is the
FS Wiki. Since it's written by the same people who visit this forum (if I may paraphrase Karajorma): It's almost like asking us directly!
As for the second part: I can think of 100's of uses for mixing the ships too. The problem is that there is no way I'd ever implement all of these uses in a single storyline... or if I tried to, the resulting storyline would be gigantic, and I'd never get done.
I'm not trying to discourage you. Far from it. I'm just saying it's probably a better idea to pick one or two ideas out of those hundreds and develop them into a good plotline, mixing only the ships you need to. Saves a lot of space and work, and makes for better storytelling anyway.