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 3-4 minutes, until translucent. Add garlic and cook 1 minute more.
03 - Add ground beef; 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 - Cook manicotti shells in salted boiling water 1-2 minutes less than package instructions. Drain and rinse gently with cold water to halt cooking.
06 - In a bowl, mix ricotta, mozzarella, Parmesan, egg, parsley, nutmeg, salt, and black pepper until smooth.
07 - Fill each manicotti shell with cheese mixture, using a piping bag, spoon, or zip-top bag with the corner snipped off.
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 remaining mozzarella and Parmesan.
10 - Cover with foil and bake 25 minutes.
11 - Uncover and bake 10-15 minutes more, until cheese is bubbly and golden. Let rest 10 minutes before serving. Garnish with fresh basil or parsley if desired.