Manila folders are a good way to keep similar materials together. Use a single folder for each book you are working on. Where you have a lot of material, use different folders for your manuscripts, correspondence, reviews and other material. Label each folder using an HB pencil. Pencil has lasted for centuries and does not damage like some inks and pens. Your label can be as simple as Book Title: Manuscripts or Book Title: Correspondence or Book Title: Reviews. Terms you normally use in your profession are fine.
Quick tips
Storing your collection
Gathering supplies
Oversized material
Special formats
Thermal copies
Small items
A final word