The colors are to help you recognize which is the roughest or coarse side, and which is the smoother side. Usually the rough side is used to get the edge of the blade close to it's final shape, and the smoother side then smoothes out the final edge. I recommend getting a book on knife sharpening, or find one of the sites on the web that do a good job of explaining this.
I'm almost guessing you already know this, and are just having a little fun. ;-)