I've read that it's ok to adjust volume levels of individual channels if you want to after running audyssey but you just don't want to make any tonal adjustments or eqaulizer adjustments to anything. I also read you should try to get your audyssey level on the bass above -10 if you can. All you would need to do is decrease the gain on the sub and rerun audyssey and repeat until you get a number above -10. I turned my gain down to 25% and still got a -12 on mine. I just haven't gotten around to messing with it yet.
I like my LFE to be really loud anyway. I turned the gain back up to 50% and the level to -3 when watching movies anyway so it's not a big deal in my setup.