Do you have access to the documentation that can be downloaded from FileConnect? This should contain the information about setting up the SharPoint scanner. This scanner allows Network Discover to interact w/ the SharePoint scanner.
I don't have my documentation in front of me to fully explain/reference it, but I would recommend reading it.
So Network Discover is for setting up the Network Discover Server and the SharePoint file is for setting up the scanner on the local SharePoint server.
Hope that helps