I run stereo subs on my 2 channel rig. Although I don't use the sub output/s rather I use the L& R outputs on my preamp to my subs. I use the DSP's on the subwoofers to correct for room nods before I run the room correction on the pre-amp...as a speaker/sub unit each side.
This works very very well for me and sounds fantastic.
I vote run stereo subs.
Orotund Desert Theater:14'x20'x10',100amp service, JVC RS620, 120" AT screen, Carada Masquerade Masking, OPPO-203 & Panny ub820, Anthem AVM60, Simaudio Moon Titan 7&5 channel amplifiers, ACInfinity Fans, L&R Polk SDA SRStl Fully built, CC 2 Polk RTA15tl in Custom cabinets Fully build, SS-BS DT BPXV, 4 Atmos 3 way Core5's, Subs-Rythmik FV25HP front 2 HSU VTF-MK5-HP back, 2 Rows of 3 Seatcraft Excalibur Lx Seats and more.