Do a search on this forum for "subwoofer" and a bunch of discussions will pop up. Joji just put one of the powered subwoofers on the carpeted ledge that covers the engine because his boxster didn't have any rear speakers. Details are here:
http://986forum.com/forums/showthread.php?t=3639&highlight=KSC-SW1
It's so tight behind the seats and under them that any decent sized subwoofer probably won't fit unless the driver or passenger's seat is brought forward permanently.