Cook the pasta according to the package directions but until slightly underdone.
In a large saucepan, warm 1 tablespoon of the oil over medium-high heat. If using fresh sausage, squeeze the meat from the casing into the pan. If using cured sausage, slice it in half lengthwise and then crosswise into ½-inch-thick half-moons. Add the sausage to the pan. Cook, breaking up the meat with a spoon (for fresh sausage) or turning now and then (for cured sausage), until well browned, 5 to 6 minutes. Remove the sausage and set it aside.
Add the remaining 1 tablespoon of oil to the pan. Add the onion and bell pepper, and cook until soft, 5 to 6 minutes. Add the garlic, sage, fennel seeds, and red pepper flakes, and cook for 1 minute. Add the tomato sauce, and cook until heated through, 4 to 5 minutes. Stir in the reserved sausage.
Heat the oven to 400ºF. Coat a 13- by 9-inch baking dish with cooking spray. Drain the pasta and combine it with the sauce. Stir in 1 cup of the Fontina, 1/4 cup of the Parmesan, and the black pepper. Mix well. Scrape the mixture into the prepared baking dish, and top with the remaining 1 cup of Fontina and 1/4 cup of Parmesan. Bake until bubbly and golden, 20 to 25 minutes.
Tip: Serve the pasta with toasted slices of Panera Bread Ciabatta spread with fresh pesto.