This program must be ran in your Age of Conan directory, in the same location as your AgeOfConan.exe file. Any other spot and it will not work. It will first scan through the Default directory to grab all the current version numbers, then it will scan all of your custom files. If the version numbers don't match, it will update it.
I strongly recommend that you only use this if:
A) You are on the Test Live server. UI modders tend not to maintain a separate mod for this so it's pretty much your only option to use UIs over there.
B) Your favorite UI isn't being updated anymore. I strongly recommend grabbing the latest version of your UI for new features and bug fixes.
Follow the individual addon's installation instructions.