01 - Preheat oven to 375°F. Lightly grease a 9×13 inch baking dish with cooking spray or olive oil.
02 - Heat olive oil in a large skillet over medium heat. Add chopped onion and sauté for 3-4 minutes until translucent. Add minced garlic and cook for 1 minute until fragrant.
03 - Add ground beef to the skillet. Cook until browned, breaking up the meat with a wooden spoon. Drain excess fat from the pan.
04 - Stir in crushed tomatoes, tomato sauce, tomato paste, dried basil, dried oregano, red pepper flakes, sugar, salt, and black pepper. Simmer uncovered for 15-20 minutes, stirring occasionally until slightly thickened.
05 - Bring a large pot of salted water to boil. Cook manicotti shells for 1-2 minutes less than package instructions. Drain and rinse gently with cold water to stop the cooking process.
06 - In a large mixing bowl, combine ricotta cheese, 1½ cups mozzarella, ¾ cup Parmesan, egg, parsley, nutmeg, salt, and black pepper. Mix until smooth and well combined.
07 - Fill each manicotti shell with the cheese mixture using a piping bag, spoon, or zip-top bag with the corner snipped off. Pack the filling evenly into each tube.
08 - Spread 1 cup of meat sauce over the bottom of the prepared baking dish. Arrange filled manicotti in a single layer over the sauce.
09 - Spoon the remaining meat sauce evenly over the pasta. Sprinkle with 1 cup mozzarella cheese and ½ cup Parmesan cheese.
10 - Cover the baking dish with aluminum foil. Bake for 25 minutes.
11 - Remove foil and bake for an additional 10-15 minutes until the cheese is bubbly and golden brown.
12 - Let the manicotti rest for 10 minutes before serving to allow the filling to set. Garnish with fresh basil or parsley if desired.