Example mkv adding video, audio, subtitles and languages for each track
Convert subtitles to UTF-8
iconv -f ISO8859_1 -t UTF-8 INFILE.srt > UTF8-OUTFILE.srt
File with French audio track and English subtitles
mkvmerge -o OUTFILE.mkv -A -S video.m4v audio.aac subtitle.srt
mkvmerge -o FINAL.mkv --language 2:fre --language 3:eng OUTFILE.mkv