What are you looking to back up, the entire system, users folders, applications folders, shared folders?  Depending on how hard core you want to get the paid for Retropect Server can do it for you, but it cost money.  Let me know what you have found and I will suggest others.  The other possibility is  to try doing it with something like carbon copy cloner (shareware I think, but well worth it).

There are other options out there, but it all depends on how much you want to backup.  If I were looking to do the cheapest way it would be the free way of partitioning out the biege hard drives (uh.. how are you doing that by the way, connected firewire drive? or PCI SATA card?).  Once partitioned you could write a simple applescript or shell script to mount drives and DITTO the files (don't cp the files, doesn't always take the resource forks).

Let me know more of what you want and I'll share what scripting knowledge I can with you.

Chris