What this post is really about is how to take the changes you've marked on your hard copy and enter them into your word processor. Maybe I was the only one doing it the hard way for years, but everyone I've asked has said that they do it like I used to--they start at the beginning and work their way through to the end.
This is how I edited my first few dissertation chapters. But executing the changes I'd already made on paper took forever because the location of words on the page kept changing as the material above became longer or shorter with my revisions. This was supposed to be a mindless, mechanical task, but I found myself reading the entire draft over again to find the places I'd marked to revise.
Then I had a breakthrough. I realized that if I started at the end of the document, the changes would only affect the position of what I had already fixed. In short, everything stayed put on the page until I got there, making it so much easier to find the problem areas and make my corrections.
Maybe this is how you've been doing revisions all along, but if not, you will be shocked how much time you can save.