+$0.02:
Based on some experiences I've had in the past performing some similar automated document scanning / processing / storage, the "weakest link" in the whole process is the process of interacting with the scanner during image acquisition. Windows is great at making, say, the selection of a printer and sending output to it a very generic process that is readily automated. However, image acquisition lacks the unified & streamlined functionality. As a result of this, depending on the application you are using and the particular scanner [and associated software] that you have, that part of the process is going to vary the most.
As others have pointed out, there are many open source software projects that provide PDF file manipulation that you can use. Also, WinBatch has the flexibility to access spreadsheets, text files [CSV, XML, JSON, etc...] and various SQL database implementations, so looking up a list of employees should be a relatively straight forward thing to achieve.