When I add the application roles offline by hand, is it saved only in my Admin Tool? Where does that information get saved in? If another developer makes RPD changes and uploads the RPD, would my permission changes get overwritten?
Yes, cnahges will saved in repository. Another developer should open RPD-file you have already changed - then he will see roles, that you added.
If another developer will upload the repository without your changes, then your added roles will be lost