Okay, I'm half way through my second cup.
On page 61 of the
Manual it says "you can adjust the level of each speaker with the built-in test tone so that the volume of each speaker is the same at the listening position." You only need to bother with this as a check to see if Audyssey got it right. So I'd Focus on setting up via Audyssey (after tweaking speaker / sub positions as needed.)
Follow it through on page 37. You need quiet to do this correctly, so pick your time accordingly. (I even shut down the HVAC system when I do it.) I always stay away from the mic (usually at the back or side of the room away from speakers, as to not interfere with the calibration.