Peter,
I see the value in using Updox and also see a value in using paperport (no monthly cost). I don't think you are using all the tools available to you in UPDOX.
If you are using Updox and say get one fax containing ten pages with results for different patients. You do not need to use paperport to separate these. Use your mouse and point it over a document. Then there will appear "Select" . Use the select button in UPDOX to choose which pages you want to import into AC (this can also be done across multiple faxes at the same time). To the left side there will be a button marked "Send ___ selections", from there you can send to EMR, send to file, send to portal, or send to email (all at the same time). That's it.
As for sending manual faxes, I would set up your MFC to scan and save to the SENDTOUPDOX folder. Anything saved to this folder automatically gets imported into UPDOX. From there you can send the fax (or import etc) and have an electronic audit trail.
Whenever I send a fax regarding a patient, I also send a copy to the patient chart via UPDOX. These get saved into the IMPORTED items section in AC in a custom category called "correspondence". This way I can see what I sent to others regarding a specific patient. From the computer you use to run UPDOX, you can also print to it like you would print to a PDF printer.
As for your doctor not wanting to log in to sign a form, you could always print what you need to have him sign and scan it back into UPDOX as I mentioned above.
