When writing an output file, MakeMKV always writes all tracks in following order:
- video track
- all audio tracks, sorted by weight. If two tracks have the same weight, they are written in the same order as they are in source file.
- all subtitle tracks, sorted by weight. If two tracks have the same weight, they are written in the same order as they are in source file.
To set a specific order for tracks, just change track weight to desired track position (i.e. "1" for first track, "2" for second, etc).
To just make sure that a certain track is first, set its weight to "0"