Hello Poohdaddy, It's been a few years since I played with sound systems, but from what I remember, sub woofers are unidirectional. They are merely meant to reproduce sounds 150 hertz frquencies down to 20. Which means, they make some noise and definately help you feel the bass. Our normal hearing is 20 hertz to 20 mega hertz, the closer you get to either end of the spectrum, the less we can actually hear them. Thus giving us super sonic and sub sonic. As far as a sub bass is concerned, box size and what optimal frequancy you are trying to attain with your sub will determine where you can mount your box. Look up the specs on your sub, figure out if you want a rumble or an audible drum beat and remember, an audible drum beat is about 100 to 150 hertz, while a rumble is a 100 to 20 hertz. You can hear and feel them both. Also, don't forget how much power you put to them. I hope I didn't confuse you. These factors will help you with your size and after the size is determined, them you can worry about mounting options. If you have isobaric speakers, they ususally take up half the standard box size. If you are worried about space, smaller speakers with low frequancy ratings can help with that. For example, instead of one twelve and a 3.5 cubic foot box, you can use two 8 inch long throw woofers in a 1.5 cubic foot box and a smaller amp crossed over at 100 megahertz. That can reproduce the sound and feel of a 12 inch sub. Good luck. I hope that was a little help.
Usually if you place them back, they produce more bass. You can face them down and should net simiar results. If you face them down, you don't have to worry about them being damaged. If it's a sealed box, you can shape it any way you want, just be sure that the internal air space is the size the sub needs. Obviously if you face them down, make little legs on the outer portion of the box to keep the subs off the ground.
As Gabe said, low bass is not directional, so it really shouldn't matter.
I have a box made by JL Audio with a JL 12w3 sub in it. It fits behind the 3rd seat. The side of the box with the sub on it is angled & almost matches the angle of the 3rd seat. The sub faces forward & it's almost a perfect fit. I had the shop put in some extra wire so I can move the box forward if need be.
Pics are available on the Armada page of my personal website: Stereo Pics