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 thoroughly browned, breaking up 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 cooking process.
06 - Combine ricotta cheese, mozzarella, Parmesan, egg, parsley, nutmeg, salt, and black pepper in a mixing bowl. Mix until smooth and evenly incorporated.
07 - Fill each manicotti shell with 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 across bottom of prepared baking dish. Arrange filled manicotti shells in a single layer over sauce.
09 - Spoon remaining meat sauce over manicotti, covering completely. Sprinkle with remaining mozzarella and Parmesan cheese.
10 - Cover baking dish tightly with aluminum foil. Bake for 25 minutes.
11 - Remove foil and continue baking for 10-15 minutes until cheese is bubbly and golden brown.
12 - Let manicotti rest for 10 minutes before serving. Garnish with fresh basil or parsley if desired.