Your sub-woofer can go anywhere you like, unlike the higher frequencies from tweeters your ears cannot discern where the sound of the sub-woofer is coming from. I would make the recommendation that it is not up against anything, since it will rattle items during a action movie.
Crutchfield.com has a decent tutorial on speaker placement --
Even if you have difficulties placing the speakers, new home theater receivers come with microphones and testings sequences that will test the acoustics of room and adjust each speaker accordingly. You would plug in the microphone, place it where you typically sit to watch the movie, run the test, and the receiver does the rest.