The question is: is it important enough for you to maintain 2 copies of the show?
Normally, you would simply mux all audio and subtitle languages into the same video file. (easily done with MKVtoolnix)
That way you can decide dynamically which versions you want to hear/read.
This obviously doesn’t work if the video tracks of the two language versions are so different, that the audio/video/subtitle synchronicity is not guaranteed.
In the latter case, you have no choice but to create two complete versions of the whole folder structure. Append the folder name of each with clarification about the language version – e.g.
/Anime //<-- folder which has been added to the Plex library
/Future Boy Conan (1978) [jap]
/Season 01
Future Boy Conan (1978) [jap] - S01E01 - Remnant Island.mkv
Future Boy Conan (1978) [jap] - S01E02 - The Journey.mkv
Future Boy Conan (1978) [jap] - S01E03 - The First Friend.mkv
...
/Future Boy Conan (1978) [eng]
/Season 01
Future Boy Conan (1978) [eng] - S01E01 - Remnant Island.mkv
Future Boy Conan (1978) [eng] - S01E02 - The Journey.mkv
Future Boy Conan (1978) [eng] - S01E03 - The First Friend.mkv
...
After scanning the library, both versions will initially be merged into the same show.
You go then to the top level of the show (easiest by clicking on the show’s title), then select “Split” from the ellipsis (. . .) menu.
Then you will get 2 identical shows. Rename the title of each to reflect the language version. (to find out which is which, take a look at the Plex media info of an episode)
Keep in mind that these will still be connected, nonetheless. If you watch S01E01 of the Japanese version, the S01E01 of the English version will also be marked as “watched”.