Use your spare tire well as a sub enclosure. If you use subs that dont require a lot of air space you can add a killer system with NO loss of space.
I have 2 bazooka EL 12's in the tire well of my 95 accord, absolutely no loss of space and it sounds good.
All you have to do is get a piece of MDF and cut it about the same size of the cover over the well. Cut the holes, and seal it in place with expanding foam that hardens and IMO sounds better than a box in the trunk. Let me know if you want pics???