I finally came up with a system for my card stock scraps. I bought twelve 3-drawer containers from Wal-Mart. In each drawer, I put a divider I made from two sheets of Wal-Mart white card stock scored and glued together.
I organize my construction paper in plastic files. Keep scraps in the green hanging folders that separate the colors. Crates also work. This makes them stackable and portable and easily used by students. No more mess and damaged paper!
If you make A2 sized cards and need a smaller mat for your card...cut the sheet into quarters and store the extra mats in a box indexed by color...especially nice if you use a specific brand of cardstock.