Plex does not handle Editions for TV Shows like it can for Movies. This leads to problems you are having with DS9.
Organize as @MovieFan suggests and also follow Plex naming requirements. You may need to Plex Dance after renaming.
/Media/Televisions <-- folder added to tv show library
/Star Trek Deep Space Nine (1993) [DVD Rips]
/Season 01
/Star Trek Deep Space Nine (1993) s01e01.mkv
/Star Trek Deep Space Nine (1993) [Upscaled Test]
/Season 01
/Star Trek Deep Space Nine (1993) s01e01.mkv
Plex will initially combine the series. You can split them apart so they appear separately. Plex will still consider them one show, so play progress, watched status, etc. will be the same. Continue Watching may also mix the shows. You may need to choose the desired version from the library instead of the home screen.
See this post: How to specify the versions names of same episod on a TV show? - #2 by FordGuy61
