Preheat oven to 350 degrees. Prepare cake batter as directed on package for 24 cupcakes. Cool completely.
Beat pudding mix and milk with whisk for 2 minutes. Let stand 5 minutes. Meanwhile, use a serrated knife to cut cupcakes horizontally in half. Whisk 1/2 cup of Cool Whip into pudding. Spoon onto bottom halves of cupcakes, using about 1 tablespoon for each. Cover with cupcake tops.
Microwave remaining Cool Whip and chocolate in a small microwaveable bowl on high for 1 1/2 minutes, or until chocolate is almost melted, stirring after 1 minute. Stir until well blended. Let stand 15 minutes. Spread onto top of cupcakes. Refrigerate for 15 minutes.