Heat the Oven - Set the oven rack to the center position. Preheat to 400°F (204ºC).
Cook the Sauce - Heat olive oil in a large saucepan or Dutch oven over medium heat. Add onion, garlic, and Italian seasoning. Cook, stirring frequently, for 3 minutes or until the onion is tender. Add the tomato paste, stir, and cook for 1 minute. Add crushed tomatoes, diced tomatoes, salt, and black pepper. Simmer and stir occasionally for 10 minutes. Season with salt and pepper to taste.
Cook the Pasta - Boil the water in a large pot over high heat. Stir in the salt until dissolved. Add the pasta, and cook for about 8 to 9 minutes until al dente, stirring occasionally to prevent sticking. Drain the pasta in a colander and rinse with cold water until it is cool. Place manicotti in a single layer on a sheet pan. Set aside.
Make the Filling - In a medium bowl, combine ricotta cheese, 1 cup mozzarella, Parmesan, egg, parsley, basil, Italian seasoning, salt, pepper, and nutmeg.
Fill the Pasta - Transfer cheese filling into a large resealable plastic bag or piping bag fitted with a large round tip. Cut off one corner of the bag. Pipe the cheese mixture into each manicotti shell (about 10). Set filled pasta on a sheet pan.
Assemble the Manicotti - Evenly spread half of the tomato sauce on the bottom of a 13 x 9-inch baking dish. Add the stuffed manicotti in a single layer. Spread the remaining pasta sauce over the stuffed pasta. Evenly sprinkle 1 cup of shredded mozzarella cheese on top.
Bake - Cover the manicotti with foil and bake for 30 minutes. Remove the foil and bake for about 5 additional minutes until the sauce bubbles.
To Serve - Garnish manicotti with parsley, basil, and parmesan cheese.
Notes
Serving Size: One manicotti with sauce.
Make-Ahead: The casserole can be assembled 3 days in advance. Bake the day you’re ready to serve.
Using Store-Bought Sauce: Add 5 cups of marinara sauce to the sauteed onions, garlic, and Italian seasoning. Simmer for 10 minutes.
Make a Meat Sauce: You can brown 1 pound of Italian sausage, ground chicken, turkey, or beef first, then simmer it with the tomato sauce for added flavor.
Storing and Reheating: The manicotti can be refrigerated for up to 5 days. Cover and reheat individual servings on high power in the microwave until warmed, about 1 1/2 to 2 minutes.