Preheat the oven to 350 degrees F. (325 degrees F for dark coated pans) Line two jumbo muffin pans with paper liners.
Blend the cake mix, water, oil, and eggs in a large bowl at low speed using an electric hand mixer. Beat at medium speed for 2 minutes, or until all of the lumps are gone.
Pour or scoop the batter into the paper liners. Bake immediately.
Bake for 20-22 minutes. They are done when a toothpick when inserted comes out clean. You can also check with your finger if the cake bounces back when you touch it, it's done.
Let the cupcakes cool completely before frosting. About 15-20 minutes.
Peanut Butter Frosting
In a large mixing bowl of a stand mixer or use an electric hand mixer with a large mixing bowl. Combine the shortening, powdered sugar, salt, cream cheese, peanut butter, and milk. You want a slightly thicker frosting with this recipe. Add more milk if needed to your frosting.
In a double boiler, combine the chocolate chips, corn syrup, butter, and heavy whipping cream. Place the double boiler over simmering water. Once the water starts to simmer, turn the heat off. Stir the chocolate with a large spoon or spatula until it is melted and smooth.
If needed, add a little more heavy cream at a time until the chocolate is smooth and shiny.
Set the cupcakes on a half sheet pan lined with parchment paper.
Cut off the tip with sharp kitchen shears or use a large star pastry tip inside the bag. Place the frosting into a disposable pastry bag using a small spatula or tablespoon.
Starting on the outside of the cupcakes, pipe the frosting in a circular pattern working towards the center until the entire top of the cupcake is covered.
Place the cupcakes into the refrigerator for about 10-15 minutes to set the frosting.
Spoon the chocolate ganache over each cupcake.
Add the pieces of peanut butter cups onto each cupcake. Refrigerate the cupcakes for an hour before serving. Refrigerate any leftover cupcakes.