01 - Preheat oven to 375°F. Lightly grease a 9×13 inch baking dish with cooking spray or oil.
02 - Heat olive oil in a large skillet over medium heat. Sauté onion for 3-4 minutes until translucent. Add garlic and cook for 1 additional minute until fragrant.
03 - Add ground beef to the skillet and cook until thoroughly browned, breaking up the meat with a spoon. Drain excess fat from the pan.
04 - Stir in crushed tomatoes, tomato sauce, tomato paste, dried basil, oregano, red pepper flakes (if using), sugar, salt, and black pepper. Simmer uncovered for 15-20 minutes, stirring occasionally until sauce thickens.
05 - Cook manicotti shells in salted boiling water for 1-2 minutes less than package instructions indicate. 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 blended.
07 - Fill each manicotti shell with the cheese mixture using a piping bag, spoon, or zip-top bag with the corner snipped off.
08 - Spread 1 cup of meat sauce evenly across the bottom of the prepared baking dish. Arrange filled manicotti in a single layer over the sauce bed.
09 - Spoon remaining meat sauce evenly over the filled pasta. Sprinkle with 1 cup mozzarella and ½ cup Parmesan cheese.
10 - Cover baking dish with aluminum foil and bake for 25 minutes.
11 - Remove foil and continue baking for 10-15 minutes until cheese is bubbly and golden brown on top.
12 - Allow the dish to rest for 10 minutes before serving. Garnish with fresh basil or parsley if desired.