I've been looking high and low for a solution to auto backup my cpanel accounts (via a few shared hosting accounts). I have two Windows servers at home that I have used to backup manually for years. I know I can backup via cron & PHP but I would need to setup 50+ files and cron jobs... no thanks. All I really need are the databases backed up.
Short of creating the file and cron job on each account, there isn't really a good way to automate them all especially without having access to WHM. There are some services out there that will pull your cPanel backups automatically but that's not to your own servers (it's to theirs) and it's not cheap last time I looked.