You will likely get the same resonance from a sub no matter which way it fires. I lively floor is not a bad thing as long as you have a dead ceiling and walls. The square room is the biggest issue but not a lot you can do about that.
I also have wooden floors and the biggest improvement I have ever made was acoustic panels behind the front speakers, sub and on the "first reflection" side walls.
I second the Subdude and if the cylinder works best for you, I say go for it.