Hi clafleur76,
As you probably know, the SSODB isn’t included in the BizTalk backup job, you can therefore back it up independently without issue.You should also be backing up your Master Secret.
If it were me, I would keep the SSO backup separate, simply so I can have better granularity on my backup jobs.
There is a Technet article that offers some more detail -see: http://technet.microsoft.com/en-us/library/ms962219.aspx
Hope this helps.
Cheers, Nick.