If you were using the housings already in place, you'd put the 6.5" woofer in the door with the 1" tweeter on the mounting for the side mirrors and the 4" mid in the back seat arm rest. However, the cross over is going to be putting your mid level audio in the back seat, seperate from your woofer and tweeter. I can't imagine the result would be good.
Just get a 2 piece component system with a 6.5" mid and a 1" tweeter. Those go in the door housings already there. Then, if you want rear fill add a pair of one way 6x9s in the rear. I'd ignore the 4" speaker in the back entirely.
You'd probably only need a single 10" sub if you wanted to go all out as well.
Bose's setup is totally unique to Bose. They run .75 Ohm speakers in order to get enough volume out of their crap. You'll need a new amp and a little adapter than converts the output of the deck into a line out for the amp.
I would NOT recommend using their amp and the deck itself can't power the speakers.
If you want to use it for a seperate 4" rear fill speaker, go ahead, but a 6x9 should be sufficient for that.
What isn't a good idea is using the mid in a three piece component system. You'll wind up with all your mid range audio coming from you rear at a different time than your highs and lows as well as dampened from the seats in between you and the speakers. The result would likely be a serious hole in the music at your ear.
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