One technique is to place the filling (in this case chocolate pudding) in a decorating bag with a small tip or a plastic bottle with tip which is typically used when working with melted candies. You can actually insert the tip right into the cupcake and fill it this way. I did try one with this method, but I could not tell how much was going in and, in the end, I wanted more filling.
I read online that you can use an apple corer to take a portion out of the middle. I do not own a corer, but I do own a juicer which works the same way.
Use a corer to remove a portion of the middle
Next, insert the filling
And, tada! I was not worried about the pudding on the top since so much frosting was being used and easily covered this up.
The technique was even easier than I thought. I really doubt I will go back to making boring old cupcakes every again!