I follow the Ashli over at purplemailbox - I have them in paperholders by size - papers 12x6 or in that range go in one. Anything less than that goes in another. I had them all in hanging folders my mfg and it was a PIA and I never really looked. Now that I redesigned them along with how I store my regular pattern paper which is in a box that holds most all of them and I flip through them to see what matches what when I'm putting a page together.
Sometimes I'll just go through the scraps and then line up the base page. C/S is still in hanging folders by color. It's easier that way.