I do it a couple combined different ways....I keep all my 'special' fabrics together, like Halloween, Christmas, velvet and satins....they all have their own Labeled boxes. Then when I was organizing my stash any fabric over a yard was wrapped on cardbaord, and stored on a shelf, for possible backing use. Before I wrapped I rough measured and put a post-it at the end of the wrap with the yardage amount, and any other notes I though was pertant like washed, should be washed, has flaws.... the rest of my stash is the folded and put into clear drawers by color, and some times theme, like grapes, sports, cars, etc.....after that I sort and package all my scraps by color......
I think something to keep in mind is one only method does not always work.....but a combination, and don't be discouraged if you are redoing again in 6 months as it is all a learning curve on works for you and how you work and sew.....No rights or wrongs in quilting.....just a life time of learning and getting just a little bit better every day....