Here is a closeup of some of the shelves. As you can (hopefully) see, I keep the full sheets on the bottom and then just put any scraps right on top. That way, when I need a piece of cardstock, I can search through the scraps first. I used to have the shelves labeled with the names of the cardstock, but as I kept getting more, it was frustrating to keep moving the labels. I keep my colors in ROYGBIV order, so instead of labeling the shelves, I created a little cardstock color keeper for each brand of cardstock that I have.
I keep my SU! cardstock in a file cabinet, and each color has it's own folder. I keep full sheets, as well as scraps, in each folder.
Here is the cardstock ring I created for all my MFT cardstock. I simply cut out each color using Nestabilities, labeled them with my P Touch, added a hole with my Cropadile and added them to a ring. This is a great way for me to keep track of what colors I have, as well as an easy way to match my colors to patterned paper.