Do you have a routing engine?
Is it the user's responsibility to say 'This PDF goes to this template'? Or do you have some classification system that stuffs the PDFs into buckets (say, by vendor) and templates are assigned to those? Can you tell the PDF parser where to extract data from based on created layouts?
So far, it's the user who would need to decide which document goes to which parser. You can send all PDFs of the same layout and structure to a defined layout in the App, but there is not a way currently to send undefined PDFs and have them identified by the software. As of July 2016, a routing engine is on our roadmap, and probably be one of the next features to add.