In a medium bowl, mix cream cheese, confectioners' sugar, 2 tablespoons milk, and 1 teaspoon vanilla extract until smooth and creamy.
Fold in 1 cup blueberries; set aside.
Cover the bottom of a 10 x 14-inch baking dish with 1 layer of bread cubes.
Spread cream cheese mixture over bread layer; top with remaining bread cubes.
In a large bowl, whisk 2 cups milk, eggs, 2 teaspoons vanilla extract, cinnamon, and nutmeg; pour over bread mixture.
Sprinkle 1 cup blueberries over bread-egg mixture.
Cover dish tightly, with aluminum foil, and refrigerate 8 hours to overnight.
Remove from refrigerator 30 to 60 minutes before baking.
Pre-heat oven to 375°F.
Bake for 45 minutes.
Remove foil and continue baking until center is set, about 30 minutes.