I would then experiment with the placement of your mains from the back wall, side wall, toeing them in, etc... The drivers should not be the same distance from the side walls that they are from the front wall, for example. Also, the more you pull them out from the front wall, the better bass resonse you will get.
Are you running them as "small" or "large"? I received better results with my sub if it was "in line" with my main drivers and in phase. Sorry for the simple questions, I just find it hard to believe you have to reconstruct your floor, and I don't think that will resolve your problem.
Do you have a picture or drawing of the setup?
