Preheat oven to 375°F. Mix all cheeses together in a medium mixing bowl. Set aside 1 cup for topping.
Cook pasta according to package directions. Drain and set aside.
While the pasta is cooking, melt butter in a saucepan over medium heat. Add flour, reduce heat to low and cook until flour turns golden brown, stirring frequently – approximately 12-15 minutes. Add salt and pepper and stir to combine. Gradually whisk in cream and simmer until sauce is thickened and smooth, stirring frequently – approximately 10 minutes. Add cheeses and stir until melted. Add pasta to cheese sauce and stir until evenly coated.
Prepare a baking dish with pan spray. Pour pasta into the dish. Top with remaining 1 cup cheese. Bake until the top is golden brown and bubbling – approximately 20 minutes.