For 1 12" sub I made a box that fit flush with the rear seats, and had a flat front panel with a grill on the sub. This allowed me to still open the cover for the battery and tire, and put stuff right against the box without worries. It acted as a wall of the trunk, plus provided some nice bass.
My most recent box is for 2 12" subs that is fiberglassed for looks not fit. I have no problems fitting everything in my trunk, but the box has to be removed to access the battery and spare. I made sure to provide enough speaker wire so that the amp can still be in its place, and the box can be on the ground outside the car in emergency situations.
eL eS has a good idea, but battery maintenance and fuse replacement for the rear distribution area requires you to take out the sub unless you do not cover the battery and such with the box.
eL, I never thought of fiberglassing the spare tire compartment, nice thinking.