The exaggerated bass is probably in the 50-100hz. range, you should be able to smooth it out a little through sub placement and x-over point setting. You will need at the very least...spl meter and test cd along with pencil and paper to make some freq. responce charts to plot your progress.
The above will give you an idea of what problems are being caused by speaker/sub placement and what problems are being caused by the room it's self. Solve as many of the room problems as you can with bass traps in at least the corners.
Subs that don't go down into the 20-30hz. range are not subs, subwoofer range is from around 60hz down to loss of the ear being able to hear the freq. (20hz. will do).
Another common problem is that many people set their sub level by ear..this causes them to turn it up until they can hear it, of course...once you can hear it..it's set to loud.