We catch faxes with page with paperport and scan with scansnap. We have a folder on the desktop called "to AC" We usually print the paperport documents to PDF with cutePDF which, by default, will save to "to AC"
The scansnap documents often we will directly import to AC, find the patient, F9 will open import items then import file, the last file (saved by date stamp) is the one we import and it will be PDF.