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!