I recently moved some stuff around in my craft room to condense things. I used to have my 8 1/2 x 11 card stock in my paper rack and then the scraps in a separate file container with each scrap in pendaflex folder and filed by color. I decided to eliminate the pendaflex file and put all the scraps in clear file folders and I keep the scraps with the card stock. This way I have to check the scraps before I cut more card stock. It's definitely more efficient.
I also created these color charts which show the colors in each row. Makes it easy to distinguish between some of the card stock colors that are very similar. I can tell which paper is Soft Sky and which is Pool Party by checking my chart.