Hmmm. I don't have enough knowledge to truly answer your question.
Here's my two cents, though. Because the setting of the PEQ ("Natural," "Flat," or "Front") is done prior to initiating the auto calibration routine, I would tend to think that you'd need to rerun the auto calibration in order to change it. If you do that, then unfortunately you would need to redo the tweaks that you just did. However, now that you have some experience under your belt, it will take you much less time. You can always write down your settings so that you can just go back in and change them again after rerunning the auto cal.
Now, you can change the equalizer setting for the center channel only without rerunning the cal - see page 75.
I know that this can get frustrating trying to set it all up, but once you've done it - you're done! Then you can enjoy it for months or years to come.