Chuck,
Well, first off let me say I have little to no experience using Adobe Acrobat, although it did come with my Scan Snap. I have messed around some with it but honestly have found Paperport to work better for me. I do not know that either will allow you to sign and move documents into a folder with one keystroke. I sign a document and then drag it into the folder I want. My staff and I pass documents back and forth frequently. I created the following Paperport folders, "Received Faxes on Server 01" "Lindsay's Folder, "Ann's Folder", "Theresa's Folder", "Physician to Sign", "Ready to Import", Refills" and "Office Documents". I am not sure I know what you mean about annotations being deleted even after being saved. I do not think I can alter the annotations I have made after I have saved them. I can go back and further annotate the document....I can even erase document text, but I cannot erase my annotations.
Again, I have little experience with Acrobat. I simply like having my documents, faxes, etc all in one place. I wish the Scan Snap were TWAIN compatible so I could scan directly into Paperport. Let me know if this helps or not.
Leslie