I had a similar setup a year or so back. I setup the VPS with CSF and setup ftp. Then created a directory to store the backup files and created a user that used this directory as default.
If you have root access you can backup accounts to this folder if you have a reseller account you could use something like whmeasybackup.com to backup accounts to this folder. whmeasybackup has an encryption option for extra security.
It's probably best to just use a Backup Hosting account rather than a VPS. You can setup a cronjob to rsync the data from your VPS to your backup account. Any provider offering backup services will do the initial configuration for free and you can request the setup to be checked now and again to make sure it's working as it should be.
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