With your Gallo stuff, I'd recommend setting your mains back to large (don't worry about that messing up the setup, it won't hurt as the channel trim and distance settings will be the same either way). Whether to use "LFE only" or "L/R+Sub" comes down to personal preference, probably - if you want the sub in the mix when listening to two-channel material (at which point it will be playing everything below the front crossover, even though that data will also be going to the Ref. 3.1's) then use L/R+Sub, but if you want the Ref. 3.1's to be on their own for music then use LFE only.

Your AV's (both the C and the M) look to go down to 55Hz, so I'd use either 60Hz or 80Hz - probably 80Hz. If you do set the sub to L/R+Sub, I'd probably set the main crossover to 60Hz, although you could also play with 40Hz. If the sub is set to LFE only, the front crossover will be disregarded.