Preheat the oven to 350°F. Line two standard muffin tins with 16 paper liners.

Place the chocolate chips in a small microwave-safe bowl and microwave on high for 45 seconds. Stir until smooth. If not completely melted, return to the microwave for 10 second bursts until smooth. Stir in the peanut butter. Let cool.

In a medium bowl combine the flour, baking soda, and salt. In a large bowl vigorously whisk the sugar, oil, egg, and vanilla until well combined. Beat in the melted chocolate chips and peanut butter. Gradually add the flour mixture alternatively with the water. The batter will be thin. Set aside.

In the bowl of an electric mixer beat the cream cheese, peanut butter, sugar, egg, and salt until creamy. Stir in the chocolate chips and peanut butter chips.

Fill each muffin cup half full with the batter. Spoon a tablespoon of the cream cheese filling over the batter. Spoon the remaining batter over the cream cheese filling. Bake for 20 to 25 minutes, or until a cake tester inserted in the center comes out clean.

Let cool completely. Melt additional peanut butter for spreading over the tops of each cupcake, if desired. Serve or store in an airtight container at room temperature for up to 2 days.