Server Slowness During Backups

I'm currently re-organising the way the accounts are structured on the server to spread the load during backups. With multiple websites backed up all at once it can cause a quite noticeable slowdown in the server while it creates the backups. By splitting the sites across multiple 'accounts' on the server that are backup up individually I'm hoping that there will a less of a slowdown during the process as each backup will be smaller.

There was some downtime on this site today and there might be some downtime for Soviet-Empire tomorrow while I do this.