Have a separate spoon for each color, so you don't end up with brown
Start with the bottom color of the rainbow - violet.
Spoon just enough to cover the bottom of your wrapper. Spread the color around to cover the entire bottom.
With your next color, try to spoon it out in a circle. Make a circle with your color, on the outer edge of your cupcake, and add a drop in the middle. This will help your spread the color without mixing the two together
You can pick up your cupcake tin, and tip it side-to-side to help spread the top layer of color.
Use your spoon to spread and fill in the gaps
If it isn't perfectly covered, don't worry. Just try to get most of it.
Continue, until you have your top color
Bake as cupcake mix directs you. Typical instructions for cupcakes is 350 degrees, 18-22 minutes