I think the problem you are experiencing is a software issue and not a problem w/ scanning itself. Let's start off by acknowledging that it is impossible to make notations on the margin of a scanned document. I'm not so sure that's a bad thing. First, anyone can make a notation on a hard copy. Second, a mortgage that will have 100 releases will have 100 notations all over the place. I remember those, and they are very confusing and it is easy to miss a release.
     In  Northampton County, PA, we have ben scanning documents for several yrs and use a system designed by Landex. When a release, assignment, subordination agtreement or any instrument related to a mortgage is recorded, a notation is placed on the actual index to reflect that occurence. The way our system is set up, we can enter the Book and Page of a recorded mortgage, hit ALT R, and all related documents will pop up on the computer screen. It is much quicker and more accurate than the old system w/ handwritten notations all over the place. A second way we can see what is going on is by doing a parcel ID search. In addition to searching by surname, we enter the Tax Parcel number, and all documents related to that parcel number will pop up. 
     If a computer system is properly designed, an imaging system is definitely the way to go. I understand some counties in PA do not have all these features but that is because the software designers did not involve searchers when they decided what to do. Fortunately, Landex did involve us, and we have a great system in ourt recorder's office. 
     I would talk to your recorder and see what you can do with your software system.   
     Take care. Great site!!!