Here's an interesting point I came across today while doing some box building research:
Make the box fit your car. Make the most of the space you have. Build it so you can still have things in the car that won't poke holes in the subwoofer. I like to fire my subs face down into the spare tire well - they are protected from the elements, and they make the most of reflected surfaces (you get a 1dB gain for every reflected surface. 3dB gain is twice the volume). This is similar to the increased sound of farting into a toilet bowl (it's so resonant!). Bass also doesn't care where it travels. Notice that when a bass-head is driving past your house at 2am, you hear bass only. Bass travels through everything, so it doesn't matter which way the sub faces, it will still sound great. Be aware, however, of phase shift (as mentioned above) when positioning the sub.