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This can be the result of two things:
Close it.
Don't do that, it says not to in the README.
It's an application, not a mod. Install it like you would for any other application.
The default location is always best, but the option to change directory is purely for people who want the manager off their main drive.
You'll have to uninstall the manager, and re-install somewhere different.
Note: You won't lose any profiles, or mods, by doing this.