I run 5 equal channels in LARGE and use a pair of subs for the x.1 signal only (crossover fully bypassed). I use my DVD Player's DAC for my main listen (audio out) and bypass my receivers DSP all together.
When I upgrade my AVR I plan on using the receivers Front L/R pre-outs to the sub's Line-In, employing the sub's crossover to help fill the bottom end of my front speakers. Hopefully this will smooth out my rooms low end response (the current graph looks like a mountain range).