If you don't like your sub response, there might be stuff you may wish to try. Go to that list first to eliminate the obvious problems:

SubwooferErrors

Like Doug917 said, "put the sub in the listening position" and go around the room to find the best response... You could co-locate them to avoid cancellation... Don't know if you're running your mains as large but make sure your phase it set properly. Start with -5db on you receiver/pre-amp sub out and then, calibrated them to be 2 to 3 dB hotter then the rest of you speakers... You should also get some tone disk and plot your room response to see if you have any peaks and/or nulls... There are tons of other stuff you could try (like getting a BFD) but start with this...

HTH
Gilles