Everything I own is someone else's scraps. Even the yards. The way I work it is to "bolt" and store the yardage pieces on the shelf. I don't have many so they're all together.
All of the smaller but still big-ish pieces and FQ's are sorted by color in plastic bins. Once I go into a project the little unusable bits go into a jar, everything else goes into a big bin under the table. Every once in a while I go through, sort it out by color and bag it up. Any bigger pieces go back to the color bins. Cutting the smaller ones down to strips takes too much time. I cross that bridge when/if I get there.