Heat the oven to 375°F. Cook sausage and onion in a large skillet for 9 to 11 minutes, breaking the meat into coarse crumbles, until the sausage reaches 160°F. Drain excess fat.
Stir in garlic and fennel for 30 seconds. Add tomatoes, water, roasted peppers, sauce salt and black pepper and simmer for 10 minutes.
Meanwhile, boil ziti in water with the tablespoon salt until 3 minutes short of the package time, then drain. Fold pasta and half the provolone into the sausage sauce.
Transfer to a deep 9-by-13-inch baking dish and cover with remaining provolone and Parmesan. Cover with foil and bake for 25 minutes.
Uncover for 8 to 10 minutes until the center reaches 165°F and the cheese browns lightly. Rest for 10 minutes before spooning into bowls.