Answer:
The choice is up to you, Ni! Most of the WS Faculty members and I separate our beads by color, too: either mixing individual boxes of crystals and stones into the same master container (or drawers in a hardware cabinet); or separating crystals and glass in one container, and natural stones in another. Mine are arranged like a rainbow: white/clear across the top, with one drawer being crystals, the next stones, then reds - graduating from light red through dark. The next is are pinks, then orange, browns, amber colors, yellows, greens, blues, violets and blacks. In this manner if I am working with a certain palette, it's easy to know where those colors are. While working, I pull out each drawer that has the colors I think I want, play with them, and then put them away. In some drawers I use small "Tic-tac"-like containers, or miniature zip-loc bags, so I can separate small sizes and shapes individually. This also makes it easy to see when I am running low on a certain item.
In the article
Setting Up Your Jewelry Making Work Space, WS Faculty member Mary W. Bailey shares several ways that supplies can be organized and stored, that are accompanied by several photographs.
Answer contributed by Dale "Cougar" Armstrong