>>But in the receiver settings,what do you do if you want to run the mains as large and still use the sub to fill in below what the mains are capable while not having the mains receive a full range signal (while playing back 2 channel CD)?

Get an HK receiver and set the mains crossover to a different (lower) frequency than the center and surrounds. I'm currently playing with mains set to LARGE, sub set to LFE + L/R, and mains x-over set to 40 hz. Sounds pretty good -- setting mains to SMALL is actually just fine for HT, maybe the best, but I still prefer to play music with the mains set to LARGE.

M60ti, VP180, QS8, M2ti, EP500, PC-Plus 20-39
M5HP, M40ti, Sierra-1
LFR1100 active, ADA1500-4 and -8