Preheat oven to 375 degrees F. Coat a 9- x 13-inch baking dish with cooking spray. In a large pot, cook macaroni according to package directions; drain, return macaroni to pot, and set aside.
Meanwhile, in a large saucepan over medium heat, melt 1/2 cup butter. Add flour, salt, and pepper; mix well. Gradually add milk, bring to a boil, and cook until smooth and thickened, stirring constantly. Add cheese and continue stirring until melted.
Add three-quarters of cheese sauce to macaroni; mix well. Spoon mixture into prepared baking dish and pour remaining cheese sauce evenly over top.
In a microwaveable bowl, melt remaining butter in microwave. Stir in crushed crackers; mix until crumbs are evenly coated. Sprinkle evenly over top of macaroni.
Bake uncovered 30 to 35 minutes, or until heated through.