Mic setup

Arguments could be made for either.
If you mix the two channels to two different levels, you can achieve something similar to a higher bitrate if you spend some time picking the best channel.
If you keep them as two separate inputs, you'll have scratch audio available in case you have noises added from the boom pole, etc.
 
Several schools of thought on this one.

I prefer recording the boom mic onto both channels, with one channel set to a lower record volume. If the primary channel overloads I have the second channel with (hopefully) clean audio.
 
Going to echo the others. One mic, two channels, -6dB difference on the second channel. There's really nothing of use that will come from recording with the built-in mic, and the safety channel can be a lifesaver.
 
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