If I have scraps that are bigger than a fat quarter but smaller than 1 yard then I wrap them around comic book boards and put them in my scrap drawers which are arranged by color. If they are a yard or more, then they go in my yardage drawers, also arranged by color. I almost never make the same quilt twice and since I like a scrappy quilt, it works for me to store my scraps and yardage that way rather than trying to keep designer's fabrics together.
Rob