This is something we're aware of when it comes to releasing something like this to the masses. At the moment you can modify your games Path and add multiple paths in the paths option in the tools menu.
There is also an option to verify files in the paths that you selected. It can be found in the tools menu. I havent tested it yet to verify that it will change every games path to the one it detects but I hope it works that way because it would make things simpler. Remember, this project started on June 4th.