My scraps are organized by size and color. 1 ½” & smaller together by color (or at least they start out that way.) Larger scraps and strips same thing. As I’m working they get all mixed up. Every so often I’ll take the time to straighten them out or some fabric I like gets lost and forgotten at the bottom.
IMHO I would wait to make the blocks and mix up all of your fabric when you start the scrappy quilt. This way the fabrics are mixed through the blocks throughout the quilt. That's just my take on it and there aren’t any rules you must follow for this.