Oh wow, talk about a can of worms opened! Here's my method, but keep in mind two things: I'm kooky in my thinking and there's no "one right way" (thank goodness). I store collections together first. Then sort by color. I started out just putting reds together and so on. But, now I'm slowly separating the colors by value.
I agree, be consistent with which ever system you choose. You can do some tweaking later, but it's so much work to start over and completely change the system. (Not doing that again!)