Making a hand drawn animated film is a huge endeavor. There's A LOT of paper involved which can quickly become overwhelming if not properly handled. To maintain one's sanity, I suggest getting organized!
First, I organize by scene. My export from Toon Boom Storyboard Pro is 75 scenes. Each scene that I open in Toon Boom Animate Pro gets its own legal sized folder…:
…that is stapled shut on the sides so nothing falls out:
Second, I create labels for the folders. It's a template containing all of the scene's important information, a helpful quick reference. I then add the specific production name and print for each scene folder:
I have found this to be the best way to keep track of all of the paper associated with each individual scene. The less time I spend looking for the papers I need, the more time I have for creating!