Let's say that I have 50GB of off site storage and my VPS has a hard drive of 30GB. If I wanted to back-up my entire VPS (take note that cPanel/WHM is installed) every 24 hours, how would I do so and which method is the best? I have noticed a lot of people use a software called R1Sync but I'm not familiar with this at all.
You don't specify the server's OS, but if it is running unix/linux I would use
rsync. It has the capability to only backup file changes and new files.
Now, if I was the one configuring it, I would have ssh on the backup server configured to use public key authentication for the webserver. I would then configure a cronjob to run as often as I needed.
The rsync command would look something like:
rsync -az -e ssh user@remotehost:/path/on/remote/host /path/to/backup/
Of course, if you put the command in cron, it is a good idea to redirect the standard output and standard error.
rsync -az -e ssh user@remotehost:/path/on/remote/host /path/to/backup/ &> /var/log/rsync-backup.log
Also, what are you trying to backup your VPS for? (hardware failure, accidentally deleted files, etc)
If you decide to use rsync, I would suggest reading up on all of the capabilities available.