Hey man,
Well, the benefit of InfoPath is that it helps you decentralize your business process. Remember when there was one Excel spreadsheet on a file share that everyone edited? Those days are over. InfoPath and SharePoint help you decentralize your data input. They pave the last mile to the data-entry doorstep and let you streamline your business process by allowing many people to work on the same set of data simultaneously.
In other words, you don't want to have everyone editing one form!!! :)
I'm a bit confused though since you say you are doing autonumbering but that each user edits the same form. That's weird man. Maybe you're data architecture is not allowing for parallel edits. If so, you need to fix your underlying schema.
I don't think creating separate "Main" databases for each user is the solution. Rather, you need to normalize your database tables so that multiple users can edit the same data without experiencing collisions. Maybe that's what you are implying with the "secondaries" term.
If you want to talk, let me know.
Later man