I have a different (much cheaper, probably way less capable) sub compared to yours, but my experience will apply equally to your scenario as well. Have you done the highly recommended "sub crawl" to determine the best placement for your sub? I used the RealTraps Test CD
to play test tones (primarily 20-29 Hz, and the 30-39 Hz sweeps) to do the sub crawl, and determined the spot where I liked the bass the best. Placing the sub there and doing an Audyssey calibration made a great deal of difference to the quality of bass, as well as the tonal balance of the overall output, compared to my previous sub position. And this is with a sub that has less than 10hrs of total play time to that point. Give it a try and let us know if it makes a difference (it will).