yeah, some people run MultEQ and say "my bass is TOO LOUD!" because they've never heard Dynamic EQ. Although, to be honest, that FAQ question mostly derives from either (1) a bug in the xx09 models which caused a screwy sub calibration or (2) learning how to offset Dyn EQ to compensate for boomy bass with cable TV and music sources.
there are others who complain "my bass disappeared!" like you. Most of the time - assuming proper calibration - that is due to two factors:
1. Your front L/R got set to "large" after Audyssey and thus no bass is getting redirected to the sub. If so, you need to adjust bass management post-Audyssey and ensure that all speakers are "small" and raise the fronts to 60 or 80Hz xover.
2. You are used to lumpy, overbearing bass, and for the first time you are hearing "flat" bass calibrated to proper reference. There might have been some nasty room mode that MultEQ XT cleaned up, so that comfortable "boom boom" you have grown used to has been smoothed out.
That said, many people like their bass a few dB hot, so feel free to bump up the SW level after Audyssey if you want. However, once you get the calibration and bass managements squared away, I would recommend you first live with it for a couple of weeks before making tweaks to see if you just need to get used to hearing flat bass for the first time.