Question / Help Problem with audio channels

Do Track 1 for Both, Track 2 for Desktop, Track 3 for Mic.

If you only do 1 and 2 when you watch the file you will only hear the first track. The way multitrack works is you can switch between the tracks if the player supports it, so for compatibility you should leave Track 1 with both sources, then split them on 2 and 3.

And don't use FLV, use MKV

When you go to edit the file you can delete track 1
 
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