Grease 24 mini muffins pans or coat with nonstick spray.
For the Cream Cheese Layer:
In a food processor, process the cream cheese, sugar, butter, egg yolk and vanilla until well blended and completely smooth. By hand, stir in the chocolate mini morsels; set aside.
Alternately in a large bowl with mixer on low speed, beat the cream cheese and sugar until completely smooth. Add the butter, egg yolk, and vanilla and continue beating until completely smooth. Stir in the mini-morsels.
For the Chocolate Layer:
In a medium microwave safe bowl, microwave the butter and chocolate on 50% power for 1 minute. Stir well, continue microwaving on 50% power, stirring at 30 second intervals. Stop microwaving before the chocolate completely melts and let the residual heat finish the job. Stir the sugar into the chocolate mixture until well blended. Let cool to warm.
In a small bowl, thoroughly stir together the flour, salt, and baking soda; set aside. Beat the egg, 1 tbs water and vanilla into the chocolate mixture until the mixture is well blended and the sugar dissolves.
Stir in the flour mixture until evenly incorporated.
Spoon about 1/2 tbs of the chocolate mixture into each mini-muffin cup. Spoon about 1 tsp of the cream cheese mixture over the tops, dividing it equally among the cups. Spoon the remaining chocolate mixture evenly over the cream cheese mixture. Set the muffin tins on a baking sheet.
Bake in the middle of the oven for 11-14 minutes or until a toothpick inserted in the center comes out clean except for the bottom 1/4-inch, which may still look moist.
Transfer the muffin tins to a wire rack and let stand until the brownie cups are completely cooled.
Gently loosen the brownie cups with the point of a table knife, then remove from the pans. Store in an airtight container for up to 4 days. or freeze for up to 1 month.