Vegas Pro preferences are kept in an area of your hard drive that is normally hidden. You can get to it using an Environment Variable %AppData%. This works in a Command prompt or with the Windows Explorer. A complete uninstall and reinstall will not affect them. All of the preferences for Sony software are under: %AppData%\SonyThere you will find your custom render templates under: %AppData%\Sony\Render TemplatesPreferences for all Vegas Pro versions are in a folder called "Vegas Pro" with a subfolder for each version number. So Vegas Pro 13.0 preferences are under: %AppData%\Sony\Vegas Pro\13.0This will have your Windows Layouts, Keyboard Shortcuts, Explorer Favorites, etc.
As I said there is no reason to back these up because they will not be touched no matter how many times you uninstall and reinstall. If you are moving Vegas Pro to a new computer, these are the files that you want to take with you.