I just finished my sewing room, here's how I did mine.
Seperate by color, the ones that are multi colored, go according to back ground. Then I have a stack for upholstry & decorator fabric(for crazy quilts). Another stack of wool, flannel, solids, muslin(bleached on the bottom, unbleached on top)and a stack for tone on tone prints. The tone on tone are seperated so I dont mistake them as a solid and screw up a project.Scraps are seperated in a 3 drawer orgainizer, according to dark, medium, and light's, with a plasic bin in top with rulers in it. hope this helps a little.