I understand that many people like to print out their manuscript and then cut up the paper into scenes and lay this out on story boards in their office. Others take the print out and hole punch the pages to fit in a large Filofax or office binder. The loose pages allow them to move the scenes around in the binder as they rearrange the scenes. While I love to use paper in my writing process, I tend to reserve it for outlining and brainstorming. It gives me a hard copy of what I’m working on that I can use as a referral beside my computer.
What I like to do with my scenes is to create a new project file in Scrivener for my revision, leaving my rough draft untouched in its original file. I break each of the chapters into scenes and keep them free of their chapter organization and lay them out in the new project file. Then switch to cork board view and I use the notebook where I wrote down all the scenes and use the meta-data labels to color code my scene files to match what is in my notebook and I type in each synopsis into the scene file’s index card. I like to label each scene with the character POV as well. Naturally, as I go through the manuscript, there are scenes there that I did not remember. I label those as “forgotten scenes” and there are places in the story line that have no scene associated with them and need to be added at a later time. I create a blank scene file, write a synopsis of what needs to be there and label it as a "missing scene".
More Here - Prep Your Novel For Self-Editing in Scrivener