First prepare your cake mix by following the directions on the back of the box. Bake your cake according to the cupcake instructions. After the cupcakes are done, let them cool in the pan for 10 minutes.
With the cupcakes still in the pan, take a knife and cut an X through the cupcakes (clear through to the bottom). Mix your Jell-O and pour it in the center of the cuts that you made.
Put the cupcakes in the fridge for about 3 hours or until the Jell-O is set. Remove from the fridge and top with Cool Whip, either flavored or use food coloring to make it any color you desire.