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So I am using the Mod organizer which is compiled for linux. Pretty sure it was this Mod Organizer 2 for Linux.
Tinker Launcher is the easiest way to do it. There is also a third party Linux "port" of MO2 you can install. Tinker Launcher is my preferred method. ProtonupQT is not where you get it from. https://github.com/frostworx/steamtinkerlaunch/wiki/Installation