The subs being placed in the backseat/trunk area is best, sub cones facing towards the rear of the vehicle, with approximately one to two feet, clearance between the subwoofer face and the rear of the trunklid/Hatch is best, as this will give optimal bass reflex when the sound waves hit the trunklid/hatch. Really depending on the speaker size would determine how far back you should consider placing the subs back. eg. 10"s = 1 foot, 12"s = 1.5 feet, 15"+ = 2 feet. (this is my opinion and I have installed quite a few systems for friends and family, I am not a "professional" audio installer though, But I am a professional mechanic.)
Hope this helps, and the box structure and materials help with refraction and reverberation of sound.
Edit side note: Sitting on top will make you feel the most bass possibly but will also distort the sound you hear from the woofers and other speakers.
This post was edited by DarrylYoder on May 10 2011 06:34pm