Transcribing Multitrack audio sources

I am trying to edit a video of some gaming footage and the software I use to record outputs my mic (Bottom channel) and desktop audio (Top channel) to two separate channels. This is great for monitoring my mic separately from my friends, but when I try transcribing to create captions it only creates them for the desktop audio (Top) source.
Since it's one recording with different audio channels, it ignores the mic audio (Bottom channel) when I try to transcribe them together or even separately. Is there a way to get it to transcribe both my mic channel and my desktop audio channel separately so I don't have to manually create captions for one of the tracks...?
Have yet to find someone with this fix.
