I am using Audacity with my MBox. I would like to be able to switch between the 2 mics I have plugged in to the 2 inputs, but the only way it seems I can record with the second mic is to record in 2 channel stereo. Is there a way to record with my second mic in mono?

I’m going with no.

It’s not that hard to split up the performance. From the drop-down listing to the left of the stereo track: Split Stereo to Mono.

Then [X] delete the one you don’t want.