i don't have a sub yet, but i have experimented with the LFE settings on my yamaha receiver a little bit. from what i gather from this thread, it works the same way as the denon.
in my current setup, the auto-setup feature ends up setting all the speakers to large, meaning that when it runs its tests, they all output a wide enough range of frequencies in the receiver's opinion. (i normally run the auto-setup and then make a few tweeks based on my ears alone, don't have an SPL meter and Avia disc yet, i'm getting there, though) the bass sounds really nice with all the speakers set to large (remember, i don't have a sub yet). when i go through and switch some of the speakers to small, the bass takes a huge hit, even if it is just the surrounds.
should i not be running these speakers as large? i don't think i ever put an excessive amount of power through them, but i do like to turn up the volume at times, (mainly for movies)
CMT-340SE2 Mains & Center, CBM-170SE Surrounds, Rythmik F15, Emotiva XMC-1, Emotiva XPA-5