I have similar questions, as I have a 10" sub and full size spare in my trunk and would like to know if its worth my while to try and sell my stock sub/spare, and if so Id like to be able to advise people properly.
It was a couple years ago, but I spliced into what was there to hook up my amp and sub very easily. I even was able to run both my sub and the stock at the same time. Of course it was so horrible with both but it did work.
I dont think that there is any wiring (except rear speakers) run to the back in pre 03's. Dont remember if the subspare has a proprietary plug or not, but you can just hardwire together. Somewhere here you can find the colors and what they are for the wires.