As strange as it sounds, I actually adjust my distances by ear after running Audyssey. Audyssey gets the distances pretty close, but I still get a big sound quality improvement by doing my by-ear post-calibration tweaks. The key thing is that I have special pink noise samples that I use that play correlated noise in adjacent channels. I then adjust the distances until each adjacent pair of speakers (plus the front left and right as a pair) images the noise convincingly dead center between them. When I do this, I change the units used in my distance menu from "ft" to "m" because I get about 3 times the granularity (0.01 m vs 0.1 ft) with units in meters.
The pink noise samples aren't suitable for setting sub distance, and I don't think one can get the best results setting the sub distance by ear. Not only that, but sub distance makes a big difference for good bass. On the other hand, this setting doesn't need to be as precise as for the speakers. Differences of 0.5 feet don't change much. Something you can try doing is temporarily adding or subtracting about 7 feet (assuming you crossover at 80 Hz) to the current setting to see if that improves things. If it does, then it probably wasn't set right to begin with. The best way to set this right involves taking measurements with an SPL meter and test tones or, preferably, a room measurement system.
Another possible reason for poor bass is placement related. Can you post a picture of your room including adjoining areas, where you sit, and where the sub is?