Melt the butter in a saucepan over medium heat. Add the onion & cook over medium heat for 5 minutes. Add the bacon & the flour, combine well & cook for 1 minute.
Whisk in the milk & chicken broth, stirring continuously. Bring to a boil. When the mixture comes to a boil, take off the heat & stir in the mustard, salt, pepper & cheeses. Stir well until all the cheese melts & is well incorporated into the sauce.
Mix together the sauce and the macaroni and pour into a greased baking dish.