Preheat oven to 375 degrees Fahrenheit. In large skillet, saute mushrooms, garlic and butter until softened. Stir in bread crumbs, clams with liquid, 1 cup mozzarella cheese, 1/2 cup parmesan, ricotta, parsley, basil, salt and pepper.
In large pot, bring water to boiling and cook manicotti in salted water until limp. Drain and rinse with cold water. Stuff manicotti loosely with clam mixture.
Spread 1 cup of marinara in each of the two 13x9 baking dishes. Arrange stuffed manicotti on top and spoon sauce evenly over noodles. Sprinkle with remaining cheese. Bake covered for 20 minutes, then take cover off and bake 10 minutes. Serve immediately.