Are you referring to the starter solution templates that com with FileMaker 12?
They are indeed separate files. The FileMaker 11 invoice starter solution included some very primitive invoice management. I'm glad to see the new starter solution does not include that, but am disappointed that the new starter solution didn't replace it with something better.
Integrating the two would be about as much work as taking invoices and adding your own stuff for managing inventory or taking inventory and adding your own stuff for processing invoices. And such a merge requires a good working knowledge of relational database design and FileMaker.
So you have the choice of either learning enough about FileMaker to create your own solution--either from the ground up or from one of these templates or searching out and downloading a system for both from a third party source.