Since we are all think differently, I would ask myself 'how do I want to see my fabric?" To me, it is all in how you see your fabric. For instance, do you see your fabric as:
Color
Design: stripes, flowers, dots, geometric, etc.
Dark, medium or light fabric?
If you have just a little stash, I would do it by color. If you have a lot of it, like I do, I stopped using the color method and started putting my stash into types of fabrics like: dots, stripes, geometric, floral, holidays, solid colors, panels, etc. I found this easier to put sets of fabrics together when making a quilt.
All the small pieces, I would put in shoe boxes with similar widths and sizes.
I hope this doesn't sound too confusing, as I said, we all think differently when putting quilts fabric together.