The standard I go by, and you can dispute this if you want, is as follows:
Facing the rear typically produces louder sound, facing the front will provide a cleaner sound.
Ported / bandpass will be louder, but sealed will have cleaner/crisper sound.
This of course depends on your subs and your amp, and this is just TYPICALLY what i've seen, doesn't mean it'll work 100% of the time. If you're concerned about the foam in the seat making a difference (and yes it will make a little bit of difference) then just fold down your seat back and see if it helps. As far as what way to face things and how they reverberate and the measurements away from the back of your car for placing the sub: most people will have a preference that they say works better, and I have noticed a difference myself, but if I remember right bass waves are not directional, meaning that they should emanate from a source outwards, but pointing them a certain direction shouldnt make a difference. That being said, hatchbacks seem to get a lot more sound when the waves are bouncing off the back glass.
I could go into all sorts of technical jargon about wave lengths etc. but what it comes down to is trying out different things to see what your personal listening preference is. I havn't built the system for my LS yet, but I will be soon. I still find it strange that I'm more interested in the sound quality than i am with show-off earth-shattering bass. I guess its just a sign that I'm getting old...