Two possibilities:
First, use a product like iPartition -- which we've tested in-house -- to repartition your external Firewire disk into a "Data" partition and a "Backup" partition of appropriate size. iPartition can do this without erasing the drive.
If that doesn't work for you, you can use a Sparse Image to store the backup. We've got a FAQ entry -- "
How do I update an image?" -- that covers this in some detail.
Hope that helps!