I removed the rod in one bedroom closet, and had my dh make shelves out of outside pressboard that are 36.5" apart. I have been saving the carboard centers that fabric is wrapped on in Joann's, and put my fabric (2 yards plus) onto them. I haven't separated them by colors yet. I don't like folding fabric and puting them in piles, as I always need the bottom one, and the piles get all messy. Also, do not keep your fabric in day light, it does sun bleach, even with minimal sun. If you put it on a shelf, I would make a curtain to protect. it from dust and the sunlight.
I put all my civil war fat q, and 1/8th's and scraps, folded neatly into a large shallow tub. Smaller than 2 yards, I have wrapped them around signboard, and are in totes. Flannel, well, I put it all in a couple of large totes (on the floor in the closet). My notions are all over the place, I can never find what I need, and I buy duplicates. My sewing room will be enlarged this spring, and it will be emptied for the construction. My goal is to organize all the notions and threads.