The Audio/Subwoofer Level defeats the Speaker/Manual/Levels setting.
Let Audyssey set your distances and Levels... you can turn it off if you prefer, but that does a great job for your basic set up. If you dial that in for main usage, but say you have a love for electronica that you want +6 over that channel-level setting, you can toggle that other on and off without afffecting your Audyssey setting.