I rip all my movies in both 720p AND 1080p. The end result is Plex shows 2 posters for each movie, which is fine. Unfortunately, there does not seem to be an easy way to tell from the poster which is which like there is in iOS. If I’m wrong, perhaps someone can enlighten me. If I’m right, developers, please consider adding.
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I'm assuming you are keeping your movies in separate folders? Plex has a method in place to work with multiple versions. When used properly films which have multiple versions instead collapse the version into one film, and then present you with an option for which version you'd like to watch upon pressing play.
See this support article for more info on multiple versions.