1. With an electric mixer, beat the pumpkin, applesauce, egg (1), and egg whites (3) on medium speed until smooth.
2. In a separate bowl, combine the flours, Stevia, sugar, baking soda, cinnamon and nutmeg. Slowly mix the flour mixture into the pumpkin mixture.
For the cream cheese filling
1. Beat the cream cheese, sugar, vanilla, egg whites (2) and flour until creamy and smooth.
2. Grease 2 muffin tins. Put a small amount of batter in the bottom of each muffin, enough to cover the bottom. Place 1 generous TBS of cream filling on top of the first layer, press down with the back of a spoon to even it out. Top with more batter to cover cream cheese filling. Liners should be ½-3/4 full.
3. Bake in a 350 degree oven for about 25-30 minutes, or until a toothpick inserted comes out clean. Cool and remove from pans.
Store in the refrigerator in an airtight container.