If you are providing shared hosting services to your customers on a VPS, I would advise you to take a look at CloudLinux. CloudLinux can help you limit the resource usage per cPanel account to prevent other websites on the server from bringing down the entire server and affecting other customers hosted on the server. CloudLinux will also allow you to easily track resource usage per cPanel account, as well as set CPU, RAM, and connection limits.
When it comes to backups, I would highly advise off-site backup storage. If you go to Backup Offers section in this forum you can find a simple FTP backup storage space and configure your backups in WHM > Backups > Configure Backups to automatically backup your data to the off-site FTP storage.
There are other solutions that can be used as well such as R1Soft. I would recommend that you speak with your hosting provider and ask them if they offer any redundant backup solutions.