I usually get cones so I use the bigger plastic drawers from Target. When my collection was small, I divided them by type: solid, variegated, silk, metallic, invisible, etc. As sections have grown, I've subdivided them by brand (FilTec Glide, Superior SoFine, etc) and then by color. I have color cards for my favorite brands and for anything that gave them away and I put marks by each color that I have so I can use that for a quick reference if needed. I usually use the color cards when ordering new thread and use the thread itself when picking colors at home.