Cook macaroni according to packaging directions. Drain and set aside.
Preheat oven to 350°. In a large saucepan, melt butter over medium heat and cook shallots until translucent. Add flour and herbs to the shallot mixture and mix thoroughly. Whisk in milk, and stir until the flour, shallot, and milk have thickened, about 5 minutes, being careful not to burn. Gradually add 1/2 cup mozzarella and Parmesan cheese to the mixture until it has all melted.