Basically, it entirely depends on your speakers. In your case, you might be able to get away with setting them at 60Hz rather than the common 80Hz, since they claim to be -6dB @ 44Hz (which realistically means -3dB is likely closer to 50-55Hz). I'd try 60Hz and 80Hz and see which sounds better. That has no bearing on what you are playing, the setting is the setting is the setting; based on what your speakers are capable of. If you had towers that were capable of getting down into the low 20s, then large might be a more appropriate setting, with the sub handling the bottom octave. So, if you want the sub for music, then small it is. For movies, there is no question you pretty much always want the sub for the heavy lifting. The goal is to provide smooth response across the entire range, so the settings should be tweaked with that in mind - properly blending the sub to your mains to get the most out of both together.
You have it backwards too IMO; for music, it can be more beneficial to set your speakers to large, to get cleaner sound, aka; no sub and no crossover. I find that is less of an issue with a system that has been Audessey EQ'ed, as it often does a decent job at least at figuring out what some of your main room mode issues are, though I've had it incorrectly set my speakers to large as well (-3dB at 55Hz).
LFE is not the same as bass; it is a separate channel with the Low Frequency Effects. BASS is still managed by the receiver and is sent to the appropriate speaker based on the setting you've chosen. Unless you have setup your system with NO sub, LFE will always go to the sub regardless of the crossover you've chosen. Bass is not directional (below around 120Hz) so you CAN have bass from surround information and your brain won't be able to tell the difference if your system is properly setup.