1For the cupcakes:
Preheat the oven to 350°F. Line two standard muffin tins with 16 paper liners.
2Place 1/2 cup of 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. Let cool.
3In 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. Gradually add the flour mixture alternatively with the water. The batter will be thin.
4For the filling:
In the bowl of an electric mixer beat the cream cheese, sugar, egg, and salt until creamy. Stir in 1 cup of the chocolate chips.
5Fill each muffin cup half full. 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. While still hot, sprinkle the remaining 1/2 cup chocolate chips onto the cupcakes.
6Let cool for 5 minutes, or until the chocolate chips are shiny, then spread to frost. Remove to wire racks to cool completely.