If they're in Dolby Digital 5.1, you will automatically have to use Dolby Digital processing. For CD's, I stay with stereo, but you can always try Pro Logic II and DTS-NEO:6.

If you want to keep the material below 80Hz out of your mains, set the speakers to small and the crossover point for those speakers to at least 80Hz (might also experiment with 100Hz just for the sake of curiousity). That will take care of in all modes except stereo bypass (in which case, the signal is passed without change, although a duplicate is processed to generate a signal for the sub if the mains are set to small) and the six channel analog input (which is taken care of by the analog bass management, which I would recommend switching to "on").

Have fun tomorrow!