My quilting stash, with the exception of the flannels are all ruler folded and sorted by background color and put into the drawers with like background colors. I have them in the drawers so that I can see each fabric that's in the drawers, without scrounging around looking for a particular piece. The flannels are also ruler folded but are in three 65 qt. plastic totes, simply because I don't have enough room for them in the drawers and I don't use them as often as the regular cotton. The NON quilting fabrics are all folded and in the same size plastic totes as the flannels, I try to keep all the like materials together in the same tote. My scraps to be cut into squares and strips are in the large plastic totes.
The smaller pieces I would go ahead and cut them according to Bonnie Hunter's method.
I'm sure that you'll get lots of ideas, so you can try different methods and see what works best for YOU.