Great answer. I hope that's the way it works.
I can confirm that it does work that way
The stuff you see in the "Parameter Check" section of the Auto Setup menu is just a "report card" of the results of the Audyssey configuration / measurements. That is letting you know what Audyssey measured as the approximate "low end" bass response of the speakers in your room.
If you ever want to reset your settings to this default configuration, hit the "Restore" button at the bottom of that Parameter Check menu.
Once you "restore" you should then see the exact same crossovers in the Manual Setup menu. As JD noted, anything you change in Manual Setup will then automatically take precedence over what was done in Auto Setup. The "report card" in the Auto Setup menu will still report the same numbers because, again, this is just a listing of the results. The "active" settings will always be found in the Manual Setup area.
Note that fiddling with crossovers will NOT impact Audyssey detrimentally, and in fact it is recommended to raise crossovers to 80Hz if they have been set lower. The Audyssey EQ filters are 100% independent of the basic speaker configuration.
For more info, I suggest you read through the Audyssey section of my FAQ:http://batpigworld.com/fadq.html#audyssey