Well you definitely want to put your sub where it works best, but that's up to the room. It might take a little bit of experimenting to figure it out, but wherever you end up subs are omnidirectional and pressurize the whole space.
Also, if you set up properly your speakers should be crossed over to your subs. They'll taper off at the crossover and won't even be producing deep bass. That's why I don't think you'll gain much, if anything, with the Ultra towers.