I don't think there's such a thing as "one best way" unless it's the one that always works for you. I'm always tweaking my organization as stash grows or needs change. I kind of enjoy the evolution of it, finding new solutions to problems.
I didn't inherit the neat gene either . It goes against my grain to be in a mess, but that doesn't mean it comes naturally to tidy up. That's discipline or it's the saving of my sanity!
I have found one thing that really helps, and that's storing fabric folded in drawers or bins with the fold up. Seeing my choices at a glance is really fun and invigorating. Stays neater longer.