I used to have a subwoofer in the rear area behind the back seat in a QLogic box.  I got tired of not being able to use it on long trips with the family where the back area was full.  I decided to route my amp output (under the passenger seat) to a custom box I made to fit under the rear bench.  It is a sealed box made out of MDF that acts as a bandpass when the rear bench is down.  The box is custom sized and angled in the back to fit perfectly.  Sounds really great!  Clean, strong bass that is hidden.  I run a mosfet Pioneer head unit to 4 JL Audio 3" two way speakers in the factory slots.  Sounds incredible once it is equilized to enhance the midrange.
 
Just my two cents.
 
Here is a link with some pictures
 
http://www.ctsr.com/vanagon/page_01.htm
 
Kurt
87 Wolfy