I have an Audio Technica Stereo Mic I want to use with my XH A1S....what are the menu settings for this. I assume Right would be Channel 2 and Left Channel 1 as it would in a audio mixer.

Your channel mapping works.
Set the Audio Setup XLR Input menu item to ON
Set the XLR Audio gain-up as needed (off preferred for better S/N if the mics have high enough output).