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Prepare cake batter according to package directions; set aside.
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In a small mixing bowl, beat the cream cheese and sugar until smooth. Add the eggs; beat on low speed, just until combined.
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Pour half the cake batter into a greased 9x13 pan; gently pour cream cheese mixture over batter. Gently spoon remaining batter over top, spreading to edge of pan.
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Bake at 325F for 70-75 minutes or until a toothpick inserted near the center comes out clean. Cool on a wire rack for 1 hour.
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Frosting: Combine the sugar, milk, butter, and egg yolks in a heavy saucepan. Cook and stir over medium-low heat until thickened.
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Remove from heat, stir in the vanilla and fold in the coconut and pecans. Cool until the frosting reaches spreading consistency. Frost cooled cake.