From prior experience, that subwoofer adjustment is a great way to override Audyssey's level settings in situation specific instances. Easy on, easy off; especially with the phone app.
I have always felt Audyssey sets the subs a little hot, especially as a music first kind of guy. After running Audyssey, I tend to turn the Subs down a little at the gain knob, readjust the level so it sounds good for most other usage, and then I can use the Sub Adjust to bump it for movies or manufactured sounds (i.e. Electronica, etc).
I confirmed through experimentation that this does override the level setting, but cannot speak towards whether it overrides DEQ or any other Aud. feature that you may use.