I've heard of people using the comment feature in Microsoft Word to do blocking and/or cues.
Also - if you have Microsoft One-Note, it enables you to write directly over a word document. Though if you're doing it in your own handwriting, I suppose that would kind of defeat the purpose of digitizing it.
I played around with a few ways of doing this when I was SMing but never found anything that saved me any time, it just created loads more work in formatting and editing.
Have you found any methods that work well?
