I am obsessively methodical so here is how I would approach do this. I would set each channel one at a time and then "fine tune" the system with both channels active. Additionally, during the "fine tuning" phase I would make identical corrections on each channel by only adjusting the frequencies that require "tuning" and make the CHANGE identical, NOT the setting. My thinking is that each channel will have different room interactions and doing it this way will preserve those differences.