It is no different to how it updates when a update is downloaded, just that you are initiating it yourself. It won't overwite any of your configs it will simply update the program, exactly the same as a normal update. Just make sure to install to the correct folder as the installer adds a \Launchbox to the location and you don't want a Launchbox folder inside your Launchbox folder. So if you just have Launchbox on the root of your F: drive just choose F: in the installer.