Since deployment of the DirectAdmin servers we've been trying to work with a third party plugin that would allow us to perform incremental backups over the S3 protocol to ensure the best performance. While working toward that effort, we opted for rsync with the --delete flag to hold us over. The --delete flag, if you're unfamiliar, simply means that if files are removed on the primary server, rsync would remove them from the backup server as well (ensuring that old and deleted data did not stay in the backups).
As of today we've begun using DirectAdmin's built-in backup system, and while not ideal, will mean that we will more consistently have backups for accidentally deleted data, which is of value. Backups will, for the moment, be consistent and plentiful.
This is not likely the final backup system that we will use on the DA servers, given that full backups eventually cause a heavy hit to system performance as usage on the servers grow. We will continue to work toward the secondary goal of strong incremental backups (which only backup new changes each time).