I know this thread is about UpDox. Just a little FYI, Adobe Reader X (Free, most people already have it), allows you to add sticky notes to PDF documents and highlight items. If you're scanning in a lot of items, I get the feeling you may already have Adobe Acrobat Standard that's included with popular document scanners like the ScanSnap S1500 and fi-6130.

PaperPort also allows you to make annotations and edit the documents. Included with a lot of MFC fax machines.

If you receive a high volume of faxes, consider getting a faxboard. PDFs will come in a folder where you can annotate and file them either in AC's imported items or an external filing system. Pretty straightforward.