do not tie an amp into the stock sub! it is self-amplified, and optimized for it's own performance, you willnot be able to squeeze anythign else out of it. THe stock sub uses what's called speaker-level inputs meaning it takes the stock speaker level voltage and uses that as signal. sending it more signal will only freak it out you willnot gain any output and you will most likely push it to clipping and beyond. Amplify your front speakers, this is good, but just do that, tri-way is an annoying selling gimmick that should be burned. If you want to hav emore bass, you're gonna need a different sub, period. If that's the case, it'd likely be just as inexpensive, and MUCH MUCH les sof a hassle to just get a seperate sub amp.
Oh, and to answer the tweeter question. they're wired inline with the stock front speakers. assuming you tap into the speaker wires from behind the deck, then you'll get everything you need there.
Mostly, before you really do anything, I'd take a step back, and evaluate what you're trying to achieve and attempt to determine if you're on the right route.