Making the sauce: Heat oil in a large skillet over medium heat. Saut� the onions & garlic until golden, about 10 minutes. Add the remaining ingredients, crushing the whole tomatoes with a fork. Simmer, covered, for 1 hour, stirring occasionally. Thin the sauce, if necessary, with a little water. Set aside and keep warm.
To make the cheese layer: Mix all of the cheese layer ingredients in a large bowl and set aside.
Cook the pasta according to package directions and drain it. Spread a small amount of the sauce in the bottom of a 5-quart casserole. Top with 1/3 of the ziti, then 1/3 of the cheese mixture and 1/3 of the remaining sauce. Repeat the layers. Top with the parmesan cheese and bake, uncovered, at 350� for 30-45 minutes, or until cheeses melt & casserole is heated through.