I'm not sure what everyone else does, or what the norm is, but I have the PEQ3 version of the Rythmik plate amp. I currently only have one subwoofer, so I'm running it in mono:
Music: Source>Music Preamp(dual RCA outputs)>
1 set RCAs to: Amplifiers>Speakers
1 set RCAs to: Sub(both LH and RH to Line In)
Movies/TV: Source>HT Preamp>
LH/RH Channel RCAs>Music Preamp (in HT Bypass mode)>Amplifiers>Speakers
Sub output RCA(Single)>Sub(LFE in and bass management through the HT preamp)