Preheat oven to 350 degrees F (175 degrees C). Line 24 cupcake cups with paper liners.
Place cake mix in a bowl, and pour in water and vegetable oil; add 3 eggs. With electric mixer on low speed, beat the cake mix with water, oil, and eggs until thoroughly combined, about 2 minutes. Pour half the cake mix into a second bowl; divide the remaining cake mix in half, and place into 2 separate small bowls.
Color the largest portion of the cake mix orange by mixing in 4 drops of red food coloring and 6 drops of yellow food coloring. Into a second, smaller bowl of cake mix, mix in 10 drops of red food coloring, 12 drops of yellow food coloring, and 6 drops of green food coloring, to color that bowl brown. Into the last remaining small bowl of cake mix, stir in 5 drops of yellow food coloring to color that bowl yellow.
Spoon yellow cake batter into the bottoms of 12 prepared cupcake cups, filling them about 1/3 full. Spoon the brown batter into the bottoms of the remaining 12 prepared cupcake cups, filling them about 1/3 full. Spoon orange cupcake mix over the yellow and brown layers, filling the cupcakes about 2/3 full. Try not to jar or shake the filled cupcakes, to avoid mixing layers.
Carefully place cupcakes into the preheated oven, and bake until a toothpick inserted into the center of a cupcake comes out clean, 18 to 22 minutes. Allow to cool.
Frost each cooled cupcake with the white frosting; place a piece of yellow, orange, and white candy corn on top of each yellow and orange cupcake. Place a brown, orange, and white piece of candy corn on top of each brown and orange cupcake.
1 (18.25 ounce) package white cake mix1 cup water
1/3 cup vegetable oil3 eggs14 drops red food coloring, or as needed – divided
22 drops yellow food coloring, or as needed – divided
6 drops green food coloring, or as needed
2 cups prepared white frosting
12 pieces of yellow, orange, and white candy corn
12 pieces of brown, orange, and white candy corn