Here's a link to the amp:
http://www.partsexpress.com/imageslarge/300-808L.jpg

Realistically what needs to be done is that you need to do some homework on crossovers and system equalization. It sounds to me like you have the subwoofer turned up a bit to loud and that your crossover is set to high. So, you are driving your sub with more midlevel stuff than you want and not enough bass. This is likely enhanced by having smaller speakers in the room which don't do much to fill in the mids as well as they should producing muddied sound and a poor cross frequency range from the mains to the sub.

I would lower the crossover frequency in the Pioneer AV Receiver (AVR) and then just spend some time tweaking and playing with things - including moving the subwoofer around the room as sub location can play a great part in impact and sound quality, as can the actual harmonics of the room.