I have forced my Fujitsu ScanSnap to scan into one of the Paperport directories via the settings. One step. No need to scan from paperport. Paperport handles the files as if they had been scanned from it's interface.
When we use the flat scanner for pictures we are forced to use the paperport interface, the Epson scan intermediary etc. The process takes 3-3 times as long as from the ScanSnap.
DrO