Putting subs in the location of the rear fill speakers in a vert won't help your bass much at all due to the complete lack of an enclosure, and I believe they are crossed at the factory amp to remove the bass anyway (I read that somewhere, someone please correct me if I am wrong). You will be better off replacing the door speakers, or better yet, get a sub if your goal is bass reinforcement. If you are worried about losing cargo area you have several options for sub placement:
1) passenger side stealth box, the downside is you lose your spare
2) Bazooka Tube (or similar), you can set it up with a quick disconnect so it can be removed quickly from your trunk.
3) JohnnyB's sub box (or similar) it sits on the pass through ledge between the trunk and the cabin so you don't lose any usable trunk space.
4) Rear seat delete, and in place of the seat you build a custom fit sub enclosure.