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 additional minute until fragrant.
03 - Add ground beef to the skillet. Cook until fully browned, breaking up with a wooden spoon as it cooks. 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 cooking process. Set aside.
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 fully incorporated.
07 - Fill each manicotti shell with the cheese mixture using a piping bag, spoon, or zip-top bag with corner snipped off. Handle shells gently to avoid tearing.
08 - Spread 1 cup of meat sauce evenly over the bottom of the prepared baking dish.
09 - Place filled manicotti shells in a single layer over the sauce base, arranging them close together without overcrowding.
10 - Spoon remaining meat sauce evenly over the manicotti. Sprinkle with 1 cup mozzarella and ½ cup Parmesan cheese.
11 - Cover baking dish tightly with aluminum foil. Bake for 25 minutes.
12 - Remove foil and continue baking for 10-15 minutes until cheese is bubbly and golden brown.
13 - Let dish rest for 10 minutes before serving to allow flavors to settle. Garnish with fresh basil or parsley if desired.