You can change the location that existing Endpoint back up to, and also change the location where new Endpoint root directories will be stored by default.
To change the location where existing Endpoint backup, yse the RBS Manager Console Application. Go to the Accounts section and double-click a user while the RBS Server is off. Edit it's Root Directory. You will be prompted to move data.
To change the default location of Endpoint' root directories (for new Endpoints), stop the RBS Server and in the RBS Manager go to Tools ->Properties. The Server Root Folder field will now be enabled and you will be able to pick the default location for new Endpoints.