the application data and the program are in separate folders. Normally they are
/My Documents/Run.GPS for the data and
/Program Files/Run.GPS for the program.
You can easily create a backup by making a local copy /My Documents/Run.GPS.Backup or by copying the folder to your PC using ActiveSync. The latter solution, though, might cause some problem with XML data files as some users reported (because ActiveSync does some conversions for some file types).