I'd recommend to let it record 3 tracks if you want to have one mixed.
For example activate track 1 for both the microphone and speakers in the advanced audio configuration.
Then only the mic for track2 and only your speakers for track3. By default in most video players you will then hear Track1 which is your mic mixed with the desktop sound, but if you want to use parts without desktop sound, or without the microphone, you could use parts of track2/3 in a video editor. (Assuming that is your plan and reason to record more than one track)