Rat,
It's fine to explore these EQ facilities if you want, but if you are using speakers like M80s, M60s, etc., and you leave the auto-EQ engaged, you are essentially undoing all the careful design and balancing that went into the integration of the respective M60's and M80's crossovers with their drivers.
So long as we continue to live in rooms and listen to speakers in rooms, there will always be room interactions and standing waves that will change the relative spectral balance of each speaker. Even sliding to another spot on your couch will alter the bass response, sometimes dramatically. If you put the auto-EQ mike in that position, then the system will adjust spectral balance for that position. Slide back to the other spot and it may sound awful!
With linear speakers like the Axioms, try placement to get the two speakers tonally alike. Putting one near a corner and the other away from corners will produce a big difference in the bass tonal balance of the two speakers, for example; moving both away from the corners will be far more effective than trying to EQ the speaker in the corner.
Auto-EQ systems may improve the sound of inferior non-linear speakers that have intrinsic gross deviations in frequency response, but in most cases, disabling the auto-EQ is advisable with neutral, linear speakers like Axioms.
Regards,
