Is this a cpanel server?
Create a /backups directory off the server root and things should be fine. If you backup to the home directory - you are backing up the backup every night. And using the normal Cpanel backups (daily) you'll have 3 copies - monthly, weekly and daily. You just don't want this anywhere inside your /home directory.
If you use the "Incrimental Backup" then rather than tarring and gzipping all the accounts in the home directory nightly, it'll just make one backup in use rsynch to update nightly ONLY what has changed.
I have one server with a HUGE account on it - and the nightly tar and gzip really send server load through the roof as they have lots of photo and video files. So I use the incrimental backup function. That sounds like what you are looking for. Just create a new directory off the web root called /backup or something.
