Fiestypixie, color is one way of sorting them. Or you could sort them according to lights and darks. If you did a checkerboard-type 16 patch quilt you would want to have your darks and lights separate so you could alternate them. You could also sort by style... like pick out the kids' prints, the batiks, the 30's fabrics, the civil war fabrics... etc. It depends on how you plan to use them.
You can check out some ideas on Pinterest by searching "mini charm quilt". Or take a look at my 'scraps' board, where I've pinned many ideas that would work in our 'candy':
https://www.pinterest.com/bonbonevans/scraps/