Hey great paperport thread! Another AC user pointed me here.
I've been using paperport similarly, but I have a couple of more tips for use which I learned from the school of hard knocks:
1) if your annotated stuff moves around in tiff, it is because you need to first SAVE the item with the scroll bar at the top of the document and way to the left i.e. showing the upper most left hand most corner of the document in the viewer, then the annotations will save to the right spots.
2) for signatures, all I did (and this is the work of a simple mind) was scan in a piece of paper with a bunch of different sized signatures on it. It sits in the main work compartment, my receive to PC to folder, and when I need a signature, I open viewer to the paper with the signatures, use the box on tool box right hand or upper menu bar to copy the signature, then go back to the paper that needs the signature, ctrl V to paste then move it to where I need it on the thing to be signed.
be sure to 'sign it' and then scroll back to upper left hand corner at the the upper left hand side of the paper

Lynn