the short answer is, it doesn't matter which way it faces. Most installs i see don't give a hoot about positioning beyond what looks cool. Usually the power levels far exceed what's necessary for good SQ as well.
If you're really serious about the positioning of it though, you could figure out the wavelengths of the frequency range that you expect your sub to reproduce and compare that to the direction it's facing to try and estimate whether the reflections off the interior will be causing cancellations or reinforcements where you're listening.
but then again... hardly anybody cares that much about that.
one advantage i can think of for a downward firing sub is the crap factor... that is to say it can collect and collide with far less crap if it is not exposed.
still a sub in the center console sounds like a novel idea. post pics once you get going!