The colour of the Poképuff, as far as I've been able to experience, means a flavor. The classical flavors Sweet, Spicy, Dry and Sour. I still don't get very weel wich colour is wich flavor. Would you happen to know, let us know too.
About the design, it means the amount of effectiveness. A simple puff won't give you as much hearts as one with cream, and so on. The more decorated the puff, the most the taste of each flavor.