First you need to install mkvtoolnix

apt-get install mkvtoolnix

The command is:

mkvmerge -o output-with-sound.mkv -A input-video.mkv soundfile.mp3

Or you can use batch variant:

find . -maxdepth 1 -name "*.mkv" -type f | while read NAME ; do mkvmerge -o ./output/"${NAME%.*}".mkv -A "${NAME%.*}".mkv ./audio/"${NAME%.*}".mka ; done

This method helps if your device doesn’t support external audio file, enjoy!