1) You don't need to change anything on the Denon, the preamp outs are hot (always on). I have the same unit and also use an external amp.
2) Porter's advise is correct and what most do. I however leave my M80s on Large. I personally prefer the sound that way.
3)After Audyssey calibration I always increase my subs (I have two) volume by at least 6db. I find Audyssey never seems to give me enough LFE, maybe it's just me or my room. You can also increase crossover point like Porter says above but do not lower it (disables Audyssey). You can set the M80s to small if you like.
