The rough version of the animation should be a shorthand version of the animation that *you* can understand, it's basically writing notes to yourself. You still should observe proper technique in rough form but you are the only person who needs to be able to decypher it for the finished animation. I'm like Jakten in that I just use black scribbles, personally I feel like assigning colors to separate limbs is often a waste of time unless you're doing something very complicated - like a guy flipping and spinning through midair.