I had to bump volume on sub for about 20% to get effects that were missing. Still, I am missing a power kick but I think Denon's sub channel is more accurate. I am hearing only low freq., probably since yamaha didn't have crossover freq. setting.If you performed a manual setup and set the levels and distances manually without the aid of the auto calibration, the distance settings you've entered may not be correctly synchronising the sub with the other speakers present? This could be one reason why the bass doesn't seem as it should be?
I'd suggest you use the auto calibration irrespective of whether or not you intend to use Audyssey room EQ correction afterward. You can simply turn the room EQ correction filtering off post calibration. The calibration will result in far more accurate analysis of the delays required to syncronise the sub with the other s[eakers. A tape measure cannot account for external factors influncing the time an audio signal take to leave the receiver and reach your listening position.
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If you don't trust the levels either then you can simply tweak them accordingly post calibration.