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
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:
Of course, if you put the command in cron, it is a good idea to redirect the standard output and standard error.
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.