Mix box cake according to directions. (For this recipe I substituted orange juice for the water called for in the directions).
Combine the cream cheese, egg, sugar and vanilla.
Place paper baking cups in the muffin tins. Put a small amount of batter in each cup (around 1 tablespoon), then put a good tablespoon of the cream cheese batter next. Finally fill approximately 2/3 full with chocolate batter.
Bake @ 350 degrees for approximately 15-20 minutes
While cupcakes are baking, make frosting.
Combine flour and milk. Cook until thick and cool completely. (For this recipe I substituted fresh orange juice for the milk).
When the above mixture is cool, add the butter, shortening, sugar and vanilla and mix until smooth. This step takes a while, so be patient. (For this recipe I addded 1 teaspoon of Grand Mariner for the vanilla and grated orange peel from one orange).