I’ve actually played with this a bunch of different ways. Plex also has the options to grab subtitles for TV shows directly and is fairly good at it. Only thing you have to be concerned about is matching the show with the subtitle content. Timing usually is an issue when commercials are edited. If you are converting movies you really need to look how the subtitles are embedded. If they are actually in the .mkv (not hard set) file, Handbrake does a really good job of enabling them in a .mp4 file. While windows media player wont necessarily see the option, VLC shows them fine as well as Plex.