Here is what you should put inside a .BAT file to convert only the audio stream from multi-channel to AAC stereo:
ffmpeg -i %1 -map 0:0 -map 0:1 -c:v copy -c:a:0 libvo_aacenc -ar 48000 -ac 2 -ab 96k %~n1-AAC.mkv
pause
Drag and Drop .MKV files over the .BAT you just created and enjoy a quick conversion that make most videos playable on Chromecast and Plex without the need of real-time decoding in the server.