Instead of using multiple users, or servers config files, I have 1 server with maybe DB 10 users. Some of the databases don't need to get backed up, is there a way to backup specified databases, and put them in a folder /export/USER instead of all /export?
I'm not sure, i I understood your issue.
I think, the multi-user mode of pMBP is exactly what you need. See documentation/MULTI_USER_MODE.txt in the pMBP ZIP file. pMBP will create sub-directories for every user.
Did you try this?