Server Backups rsync vs plesk

[breun]

I think we are going to stick with rsync, I just have a query regarding Mysql, we are using an expects script early in the morning to copy the /var/lib/mysql/ directory. Should I be shutting MySQL down first?

It's definitely not safe copy the MySQL data directory of a running instance. Instead of shutting down the primary instance you could also use SQL dumps or even set up replication.