Preheat the oven to 375°F.
2In a large sauté pan, heat 1 tablespoon of olive oil over medium heat. Add the onion and cook, stirring frequently, until the onion is soft and lightly golden, 3 to 5 minutes. Add 3 cloves of garlic, 1 teaspoon of salt, ½ teaspoon of Italian seasoning, ½ teaspoon of black pepper, and the red pepper flakes. Cook until fragrant, 1 minute. Add the ground beef and cook, crumbling the meat with a wooden spoon, until the meat is no longer pink.
3Add the crushed tomatoes and bring to a boil. Reduce the heat to medium-low and simmer the sauce until thick, 15 minutes. Remove from the heat and stir in 2 tablespoons of parsley.
4Meanwhile, bring a large pot of salted water to a boil. Cook the manicotti tubes 2 minutes less than the package instructions. Drain well, rinsing under cold water.
5Place the spinach in the center of a lint free kitchen towel. Pull the four sides up to make a bundle and squeeze very well over the sink to remove as much moisture as possible. Transfer to a cutting board and finely chop.
6In a medium bowl, combine the ricotta cheese, cottage cheese, 1 ½ cups of mozzarella, egg, ½ cup of parmesan, ¼ cup parsley, nutmeg, the drained spinach, the remaining 2 cloves of garlic, ¼ teaspoon of salt, ½ teaspoon of Italian seasoning, and ¼ teaspoon of black pepper. Spoon the mixture into a zip-top bag.
7Spray a 13-by-9 casserole dish with cooking spray. Spoon 2 cups of meat sauce into the prepared dish.
8Using a pair of scissors, cut the corner of the zip-top bag. Pipe the cheese filling into the cooked manicotti, arranging the filled manicotti into a single layer in the dish. Spoon the remaining sauce over the manicotti and cover the dish tightly with foil.
9Bake until bubbling around the edges, 40 to 45 minutes. Uncover and sprinkle with the remaining 1 cup of mozzarella and ¼ cup of parmesan. Bake until the cheese is melted and golden, about 15 minutes more.
10Remove the dish from the oven and let stand for 10 minutes before sprinkling with the remaining 2 tablespoons of parsley and serving hot or warm.
