It is most important to keep your floss out of the light, to prevent fading and UV damage and also to keep it safe from insects, pets, dust and other things that can damage or contaminate your floss.
Further organisation depends on how you use the floss. If you mainly stitch commercial patterns then storing by code number and manufacturer makes it easy to find specific threads. If you stitch your own designs or make lots of adaptions to published patterns then it is probably best to store floss within color families. Bundle your floss following your favorite colour wheel/card and then perhaps group tints, shades, pure hues and tones separately within the bundle embroidery.
Personally I dislike winding floss around things like cards or pegs; the creases/bends can damage the threads. I make easy pull braids from floss cut into useable lengths, these store neatly in bags or drawers. There are also plastic holders that store full skeins neatly. One method requires time and the other money.