Scanning the microfilm was infinitely easier than other copying processes. Of course, scanning the "title" page of the record (also shown in this post) was an integral part of tracking where I obtained the information.
I also like to write down notes I take while making digital images of the microfilm. Those notes I then take to one of the book scanners in the library. That image goes in the same folder as my digital scans from the microfilm. I make notes about what image numbers are from what record, what year, etc. In many cases European church records have no page numbers and these notes help me keep track of what is actually on each image. My notes always contain the name of the film to prevent confusion as well and I try and scan them as soon after creating the images from microfilm as soon as possible.
I really enjoy using the scanners while I am at the Family History Library, but one has to stay organized or your files can become extremely unorganized.