For my 2 channel CD input, I set my mains to "Large" with crossover at 35hz. Then set Xtra Bass = On. The sub fills in the lower octaves nicely.
HT media comes in through my DVD input. Here you have several options. I set my mains to "LARGE" so they can play full range. Sub crossover at 80hz for the LFE channel. My surrounds are set to "small" which I believe makes then play only 80hz and higher.