The best method for perfect bass that I have found to date is with Audyssey XT-32. Here are the caveats:
1. Make sure you can bypass the main speakers and only have the subwoofers eq'ed. Marantz allows this in both the 7700 and 8800 series pre-amps.
2. Make sure you follow instructions at all listening positions.
3. Make sure you select "bypass mains" in the menu.
4. Double check whether you used dynamic eq or not. Dynamic eq sets a great house curve for movies, and can be fun on AC/DC style rock, but for the most accurate, deep bass, set it to flat.
Doing the above has our EP800's flat to 11 Hz in room (yes we measured it and posted the curve at Home Theater Forum) without the EQ interfering with the performance of the main speakers.