Anything larger than about 1/2 yard is folded in half and then in half again (like it is wrapped on a regular bolt in half once) goes onto comic book holders and is sorted on bookshelves standing up by color.
Then my fat quarters are folded all the same way (in half then in 3rds) and are stored in side table drawers by color.
Now my scraps are sorted by shape and colors. All longer strip strips in one shoe box and all squares/rectangles by colors and sizes SML in another shoe box.
My goal this year (17 that is ) is to use a lot of scraps. Right now I am working on a rainbow scrappy log cabin (13 twelve inch squares are done). I am trying NOT to cut into my longer pieces, but to use scraps and pieces of fat quarters.