In a large pot of boiling salted water, cook rigatoni until tender but still a little firm, 10 -12 minutes; drain. Rinse under cool water; drain well.
In a large saucepan, heat oil over medium heat. Add onion and cook 3-4 minutes, or until soft. Add the sausage and cook, breaking up lumps of meat, 6-8 minutes, or until lightly browned. Pour off excess fat (I would leave it in for flavor).
Add tomatoes with puree, water, basil oregano and parsley to pan. You may also want to add '/4 cup of dry red wine. Bring to a boil over medium heat.
Reduce heat to low and cook partially covered for about 25 minutes.
Uncover, increase heat to medium, and cook, stirring occasionally, until sauce thickens, 8-10 minutes.
Preheat oven to 350 degrees. In a large bowl, toss pasta with 2/3's of the sauce. Stir in mozzarella cheese and 1 cup of Parmesan. Pour pasta into a baking large dish. Cover with remaining sauce and Parmesan cheese.
Cover with foil and bake for 25 minutes. Uncover and bake an additional 10 minutes until bubbly and lightly browned on top.