Heat oven to 375°F. Cook sausage and onion in large skillet 9 to 11 minutes, crumbling coarsely, to 160°F. Drain excess fat.
Stir garlic and fennel 30 seconds. Add tomatoes, water, peppers, sauce salt, and black pepper; simmer 10 minutes.
Meanwhile, boil ziti with tablespoon salt to 3 minutes short of package time; drain. Fold pasta and half provolone into sauce.
Transfer to deep 9-by-13-inch dish; top with remaining provolone and Parmesan. Foil-cover; bake 25 minutes.
Uncover; bake 8 to 10 minutes until center 165°F and cheese lightly browned. Rest 10 minutes before spooning into bowls.