Setup is:

@All
..Main (property "@All NOT Versions")
....Masters (Colourcoded to indicate images that have a Version)
..Versions
..All your normal categories from here on

You don't assign images to Main directly, i have it sealed.

I assign an image that is a version of another image ONLY to the category Versions.
This way it will not show up in the normal categories. You find it by running the VersionFinder script on an image in Masters.

To test the setup you can leave your Versions assigned to the normal categories as well, the script will work regardless.