This is normally done with virtualization, I guess that's what Digitalocean uses, or you use LVM or another filesystem which supports snapshots like btrfs on the server. This is not related to the use of ISPConfig btw, such snapshots are done on a lower level.
When you use ext4 without LVM and you also don't run the ispconfig installation within a VM on your server, then you don't have snapshot backups. In that case, use a conventional backup software with support for incremental backups like duplicity.
