Preheat the oven to 400F.
Put the grated Fontina and Cheddar cheeses in a bowl and pour the milk over, stirring so most of the cheese is submerged. Let this sit 30 minutes to an hour, until the cheese starts to break down.
Put a large pot of water on to boil, add some salt and the pasta. Stir while the water comes back to a boil and cook on the low end of the recommended cooking time (9 minutes for the ones I used). Drain into a colander.
Heat the butter in a small skillet and stir in the bread crumbs. Cook over medium low heat until the crumbs are toasted a bit, about 3 minutes. Spread some more butter around the bottom of a 9"x9" pan (or equivalent). Coat the bottom with a thin layer of the bread crumbs, reserving most for the top. Mix 1/2 cup of the grated Parmesan into the rest of the bread crumbs.
Put the cheese and milk into the pan and cook over medium low heat until the cheeses are melted. Stir in the other 1/2 cup of the Parmesan cheese.
Put the macaroni back into the pan with the cheese sauce and stir until well coated. Pour into the baking dish and spread evenly, then top with the rest of the bread crumbs.
Bake about 20 minutes.