Preheat the oven to 375°F with a rack in the center position.
Bring a large pot of water to a boil over high heat and salt it. Cook the ziti, al dente according to the package instructions. Drain.
Meanwhile, set a large Dutch oven or stockpot over medium-high heat. Add the sausage, onion and garlic and cook, breaking up the meat with a spoon, until the meat is browned and the onions are softened, about 8 minutes. Drain off any excess fat into a small bowl, discard.
Add the marinara sauce, tomato sauce, salt, Italian seasoning and heavy cream, stir until combined. Stir in the cooked ziti and 1½ cups shredded mozzarella.
Transfer the pasta mixture to a 9x13 baking dish.
Top with the fresh mozzarella slices and remaining ½ cup shredded mozzarella, cover the baking dish with foil and bake for 20 minutes, until the pasta is tender. Remove the dish from the oven, discard the foil and sprinkle with the Parmesan. Return to the oven uncovered and bake for about 5 more minutes, until the cheese is melted and the sauce is bubbling.
Serve sprinkled with chili flakes and fresh basil.