External Backups

After purchasing two 1 TB Iomega eGo desktop drives for render space (I originally intended to create a software RAID 1 set) I decided that I would prefer backing up my 250 GB '09 Mac Mini (my editing machine, two Vertex OCZ SSDs striped together) to a partition. I cut 105 GB from each drive, so I have 210 GB of space partitioned for backups, and it's running on Time Machine. My question was about the remaining space. I again considered RAID 1 for the remaining 895 GB, but the Iomega drives came with Data Backup 3 from Prosoft, and I decided to use that instead, so that it would be an *actual* backup. If I have it backing up one external to another via FW800, does the computer need to be awake? The software is installed on the internal SSDs, but I could do I clean reinstall on one of the drives if that would mean leaving the computer off; otherwise, is there a script for waking up the computer before backup and another for putting it to sleep afterwards? I think this would be more effective than a sleep schedule - Data Backup 3 has the option to run scripts before and after backups. Thanks in advance.