Preheat the oven to 350 degrees and add muffin liners to the muffin pan.
In a mixer, add eggs and milk. Beat together until eggs are mixed in. Add in softened butter and sugar. Mix until combined. In a separate bowl, add flour, cocoa powder, baking soda and salt. Mix. Slowly add the dry ingredients to the wet ingredients while mixing on low.
Spoon the batter into the muffin liners. I usually fill them to the top. Bake for 14-16 minutes. Check doneness with a toothpick.
Allow the cupcakes to cool and then using the back end of a spoon, remove a small circle from the cupcake about halfway down from each cupcake. In a bowl, mix peanut butter and cream cheese. Place this in a ziploc and cut off one of the corners. Fill each hole with peanut butter.
In a mixer, combine softened butter, marshmallow fluff and confectioners sugar. Mix on low until the sugar is mixed in and then increase the speed to medium until the frosting forms and becomes thicker. Add frosting to a pastry bag. Squeeze the frosting out of the bag in a circular motion on the cupcake until it comes to a peak. Serve immediately.