I believe the remote backup feature in cpanel is to allow the user to tar.gz either their entire "system wide" (backup) -- which includes crons, dbs, etc., and can be restored on ANOTHER cpanel system.. There is also the option to tar.gz backup the files only, and upload them remotely via ftp or scp.
Or, you can simply stop one DB, click on backup db, and get the .gz of it -- import/restore it to the new system, and start everything back up.
Hope this helps.
-Merlin