If every now and then you want to run you system without a subwoofer.
Set your front speakers to Large in the AVR menu to allow full-range audio, and set the Subwoofer to Plus (or "Double Bass" or what ever pioneer refer to it as ) to have the subwoofer augment low frequencies even when front speakers are set to large. Then low/high pass the subwoofer to around the 50-40hz mark within the amps settings. also make sure night mode has been engaged, this will strip the system of any bass.
Or if you're still having problems and there second hand units or have been used in the the past with different equipment rerun the auto calibration as this will certainly affect bass performance and sound to a very very large degree.