I am assuming you are doing the importing into Updox. At the time when the document is assigned to a category (by the MA or whoever) there is a check box they can click says "sign off".
So, you have to tell that person to click that check box for items you have signed physically and then they will not appear in your inbox "to sign". You could also scan in all the physically signed papers as one "job" in Updox and all the unsigned stuff as another job just to separate it in the Updox workspace.
At my office, stuff that has come in on the fax (into Updox) usually is not something I have seen and physically signed. So, to make it easier and reduce errors by the MA, they sort all the documents in Updox to show faxes first and scanned items later. That way the "un-seen" items get processed first.
