add audio track to mkv

http://savvyadmin.com/add-stereo-audio-tracks-to-mkv-files/

mkvmerge -o Cool.Movie.New.mkv Cool.Movie.mkv audio.ac3

or

mkvmerge -o "Cool.Movie.New.mkv"
--language 1:eng
--track-name "1:Cool Movie (MPEG4)"
--default-track 1:yes
--display-dimensions 1:40x17
--language 2:eng
--track-name "2:Dolby Digital 5.1 (AC3)"
--default-track 2:yes
--language 3:eng
--track-name "3:English Subtitles"
--default-track 3:no
-a 2 -d 1 -s 3 Cool.Movie.mkv
--language 0:eng
--track-name "0:2-Channel Stereo (MP3)"
--default-track 0:no
-a 0 -D -S audio.mp3
--track-order 0:1,0:2,1:0,0:3

Check the output:

mkvmerge -i Cool.Movie.New.mkv