Use a desktop player like GitHub - clsid2/mpc-hc: Media Player Classic or others which allow you to quickly adjust the delay between video and audio tracks, to determine the number in milliseconds which your commentary track needs to be delayed so it syncs up with the video.
(in MPC-HC you use the + and - keys)
Once you have this number, get MKVtoolnixGUI
Use its default “Multiplexer” mode.
Drag the movie file into the upper, left field.
Do the same with the single audio track file.
Now go to the field below and assign the proper language to all audio, and subtitle tracks.
Add a name/track title to your commentary track and make sure it sits below the “proper” audio track(s). Put the determined delay into the marked field (if a delay is actually necessary).
The title will later appear in Plex when you select the audio track for playback.
