I keep my fabric separated by color, except that I keep:
- a bag of selvages cut from yardage
- a basket of "strings" - strips of many widths and lengths, divided by light and dark
- a box of 2" squares of all colors
- a box of 2.5" squares of all colors
- a miscellaneous box of half-square triangles of all colors, divided by size (different sizes are in baggies
Do whatever works for you!