Melt 1 stick of butter in a saucepan. Add the onion and sauté until translucent, about 3 to 4 minutes. Add the milk and cook until heated through. Add the cheese gradually, stirring constantly, until it is melted and the sauce is smooth. Place the macaroni in the prepared baking dish. Pour the cheese mixture over the macaroni and stir to coat the macaroni evenly.
Melt 1 tablespoon butter in a skillet over medium heat. Add the bread crumbs and sauté until lightly browned, about 2 minutes. Sprinkle the crumbs over the top of the macaroni and cheese.
Bake for 30 minutes, or until the top of the mixture is golden brown and the cheese is bubbling. Let the macaroni sit for 15 minutes before serving.