Preheat oven to 350°.
Line 16 muffin cups with foil or paper liners.
Prepare Cheese layer: Beat cream cheese in bowl until smooth.
Beat in sugar and egg until blended.
Prepare Cake Layer: Mix together flour, sugar, cocoa powder, baking soda and salt in a medium-size bowl.
Whisk water, oil, egg and vanilla.
Stir into flour mixture. Stir in half the chocolate pieces.
Fill prepared muffin cups half full with chocolate cake batter.
Using remaining cake batter and all of cream cheese batter, spoon batters, side by side over bottom cake layer, creating a top that is dark and white.
Sprinkle tops with chocolate pieces. Bake in preheated 350° F oven for about 30 to 35 minutes or until wooden pick inserted in center comes out clean.
Transfer pan to wire rack to cool for 10 minutes. Turn cupcakes out onto the rack to cool combpletely.Servings: 2 dozen cupcakes