I use decorative boxes - Joann's and Tuesday Morning sell them as well as other stores. They have lids that lift up. They are on shelves. These hold all the small (1/2 yd or less) pieces. They are sorted by small print then large print. Then by color. I do a lot of applique so this works best for me.
The larger fabrics are larger boxes. I label the boxes too. The only problem is that I can't see in the boxes, but I have learned what holds what - most of the time.