as far as the trunk of my Gen 5.5, i found the best way to face a subwoofer in terms of bass response. here's my setup: a single 10" Alpine Type R sub in a 0.65cuft sealed box, powered by an Alpine amp mono 400W RMS. i took out the rear deck speakers for better bass flow into the cabin.
most people place the box against the back seat and face the sub to the rear. with that setup, i get good bass at certain frequencies, but cancellation at others. i suppose its the acoustics of the trunk. the worst response is with the box against the back seat and firing forward. i tried all sorts of locations and firing directions, with mixed results.
the BEST overall results came when i put the box in the rear corner (it doesnt matter, left or right) near the tailight, with the sub firing UP. not only did the bass hit the hardest there, but ALL the bass notes hit. the lower, mid, and upper bass notes played well. i tried different types of songs and music, and the bass was consistent.
try it for yourself if u have a similar setup. i hope this helps.