re:
Within the SBS console, can you designate a drive/directory in which to back up to? If the answers yes, then the answers yes for your question above. Partitioning the Backup Hard-Drive will work.
However, if other important stuff is backing up, chances are you won't be able to partition your drive safely until that finishes.
If you can't designate the drive or directory in the console, then you may need to look at getting another hard-drive especially for the SBS backup. I'd go for the later, at least you have separated your information in event of failure.