PrP - Audio Channels...

When recording you will patch the boom mic into Input 1 (primary) and the on-board mic into Input 2 (safety).

On the timeline you will see both sources of audio, they will be slightly different and therefore competing with each other.

When you edit you will only use one of the sources, for the most part this will be the boom microphone. The on-board mic is a safety and can be used if something goes wrong with your primary audio source.

This two step will show you how to do this:

The Modify Clip box opens, it will look similar to the image .
Select the L check box on clip 2 (both clips should be selected under L). This will create a dual mono track, which is what we want.