01 - Preheat oven to 375°F. Lightly grease a 9×13 inch baking dish.
02 - Heat olive oil in a large skillet over medium heat. Sauté onion for 3-4 minutes until translucent. Add garlic and cook 1 minute more.
03 - Add ground beef to the skillet. Cook until browned, breaking up with a spoon. Drain excess fat.
04 - Stir in crushed tomatoes, tomato sauce, tomato paste, basil, oregano, red pepper flakes, sugar, salt, and pepper. Simmer uncovered for 15-20 minutes, stirring occasionally.
05 - Boil manicotti shells in salted water for 1-2 minutes less than package instructions. Drain and rinse gently with cold water.
06 - Mix ricotta, mozzarella, Parmesan, egg, parsley, nutmeg, salt, and black pepper in a bowl until smooth.
07 - Fill each manicotti shell with cheese mixture using a piping bag, spoon, or zip-top bag with corner snipped off.
08 - Spread 1 cup of meat sauce over the bottom of the baking dish. Arrange filled manicotti in a single layer over the sauce.
09 - Spoon remaining meat sauce evenly over the pasta. Sprinkle with remaining mozzarella and Parmesan.
10 - Cover with foil and bake for 25 minutes.
11 - Uncover and bake for 10-15 minutes more until cheese is bubbly and golden. Let rest 10 minutes before serving.