Just a note, and I realize I'm replying a year later, but my solution for multiple audio-tracks was to do this:
- In the Setup -> Transcoders Tab I made a copy of the default video transcoder and called it Commentary 1
- I added the -map 0:0 -map 0:2 to the ffmpeg command to the Commentary 1 transcoder I made above.
- In the Setup -> Players Tab I selected Player 1, and clicked Clone player
- From the dropdown, I selected the newly cloned player (that may be called Player 2, depends on your config)
- I changed the player name to Commentary 1
- I disabled the default video transcoder from the Active Transcodings and enabled the Commentary 1 transcoder I added above.
- Now when I want to play a commentary, I just pick the Commentary 1 player instead of the default.

This works pretty well!
Thanks eger for the ffmpeg switch...I would have never gotten that on my own.