I've thought about doing something like this using a pair of subs. I took some measurements and tried to sketch out some feasible enclosures. Here are the most likely problems you'll run into:
(1) Box design - It's not the easiest thing to put together a bandpass box that will sound good. You'll definately want to put a lot of thought into this, as hours and hours of work might be all for naught.
(2) Space - The actual logistics of the woofer placement will eat a ton of trunkspace unless you can get really creative. However, a single sub should be much easier as opposed to the pair that I was considering.
(3) Permanence - Are you even going to be able to access the spare tire with that sub enclosure in there (assuming you're planning on attaching it to the underside of the rear deck)?
Not to be discouraging either, but this project will need quite a bit of engineering and fabrication to surpass putting the sub in a sealed box in the trunk and loading one of the rear corners.
I'd suggest taking some measurements and see what kind of enclosure you can come up with that will work with either of those subs to see how feasible it is.
-C
