My batiks are separate, by color; my solids are separate, by color range; my prints are separate, by color; my fused fabrics/scraps are separate, all together, flatly stacked. All are in clear 28-quart bins unless a full bolt was purchased. I don't buy pre-cuts and I don't pre-cut any yardage or scraps. I keep batiks separate because when I am looking for something, I look by fabric type first, then by color within the type.
Sorting fabric is just like sorting paperwork. Think about how you will be looking for it and 'file' it whatever way makes it easiest for you to find.