I will try to be as simple as possible. The crossover frequency for each speakers is the point where the low frequencies are handed off to the sub. It is not just cut off at that frequency, however, there is a slope or gradual handoff to the sub.
What you call the crossover setting for the sub after running setup (80hz) really isn't a crossover setting, it is really what is called a low pass filter setting. Not sure why receiver mfg's are including that these days. Anyway, you can keep that at 80hz, or even bump it up to say 120hz. Even the folks at Audyssey say there is some movie material that goes above 80hz.
Back to the speakers, as I have mentioned in other threads. Audyssey measures each speaker in "your room" and looks for the
-3dB point for each speaker and reports that back to your Denon receiver. Denon desides if a speaker is going to be called large or small, in this case they follow 40hz as a rule. So any speaker above that is called small, and speakers like the 80's can often be set to large because they can produce material down that low.
When you have a sub, you still want to set all your speakers to "small" and adjust the crossover accordingly. I would try bumping up the 80's to say 60-80hz and see what you think. The other speakers look fine to me based on what your saying.
You never want to decrease the crossover setting after running Audyssey, as that gap won't get corrected by their filters.
What you say is true about the freq knob on the sub, you want to get it out of the way, since your receiver is handling the management for each speaker.
