Ideally, you don't want the sub pushed right up against anything. It's not just a matter of the speaker cone physically hitting something (which is obviously a no-no), or about the "volume" of air, so much as the freedom of the air to move. If your sub is just an inch from the back of a seat, the air in front of the speaker has it's flow restricted. In this case, you're actually losing energy through coupling to the seatback. In other words, you're using some amplifier power to vibrate the seat instead of make bass sound waves in the air. And yes, the seat foam is absorbing energy also, lowering overall efficiency. You will never see a well-designed system with any objects near the cones of the woofers, you want them firing in as close to free air space as possible.
That said, wedging your woofer under the rear seat is never going to be ideal, and I don't think it's going to particularly matter which way it faces, up or down. Down-firing with a generous clearance under the speaker is probably the best of these two options, if there is a sub with shallow enough mounting depth to allow it. I saw someone here did a custom fiberglass box with a forward-firing woofer between the two back seats (like a center console). That is going to beat any under-the-seat solution, but of course it's not for everyone.
I have the lazy man's SQ subwoofer system right now: a 12" Infinity Kappa Perfect in a sealed box strapped into the rear passenger side seat. It looks totally ghetto, but for sound quality it is as good as it gets. Next summer I plan to do a custom box for the rear footwell which takes up all the underseat space and the normall passenger foot wells. It will be years before my oldest child's feet will touch the ground (4-yr-old in a booster), so there is plenty of time to use that space for subs, probably two 10".