I do several things. One..my fabric is folded as if on a short bolt and then placed on it's side in a clear tub of like-colored fabric so that I can see all of the material in that tub with one glance. I have tubs for my reds, greens, browns, blues and so on. When I start a project, I pull all of the small bolts out and place them in a small tub so that I have everything together. (I usually have about 4 or 5 projects going at the same time so I stack my project tubs on top of each other.)
I also have my fat quarters and anything less than 1 yard folded on a small size bolt board. (My husband cuts the bolt boards for me out of poster board.) I have about 3 long but not tall tubs with my fat quarter tubs with all of my fat quarters. I do try to have the organized by color but I have several different colors in the same tub.
I have my rulers/ scissors and cutters hanging on a peg board. That seems to help me keep them organized.
I hope this helps.