Q: ... Separate/select audio channels ...

Final Cut Server (and XDCAM Transfer) aren't set up to adjust what has been recorded (there's not even a volume control).

Just open the computer's Sound system preference pane and pan the output all the way to the left.

Of course if you are going through a mixer you can just mute channel 1, or if you're wearing earphones take the one out of your right ear...