I would put them in separate folders. You cant split them apart unless you do. after splitting apart just edit name in metadata so you can tell the two apart (add the language or whatever to name)
Yu-gi-oh Duel Monsters [English]/Season ##
Yu-gi-oh Duel Monsters [Japanese]/Season ##
for files you have that span 2 episodes if you do not want to cut into two files the only thing you can do is name like below. but this is not particularly great honestly (Something I want us to do better). It will list each episode separately but playing either one will play the same file from beginning to end but won’t mark the other watched. Of course i dunno if number of episodes it the same so this might not matter when you split apart.
Yu-gi-oh Duel Monsters [English]/Season02/Yugioh Duel Monsters S02e03-e04.mkv
https://support.plex.tv/articles/200220687-naming-series-season-based-tv-shows/
