Cook the manicotti according to the package instructions; set aside.
Meanwhile, preheat oven to 350°F. Lightly grease a 13x9 baking dish. Spread 1 1/2 cups of marinara sauce in bottom of dish; set aside.
In a large skillet, brown the ground beef along with the onion, garlic powder, Italian seasoning and red pepper flakes (if using). Season to taste with salt and pepper. Crumble the beef with a potato masher until cooked through and onion is softened. Drain of excess grease and set aside to cool.
In a large bowl, mix the ricotta, 2 cups of mozzarella and parmesan cheeses. Add the beef and stir to combine. Season to taste with salt and pepper.
Transfer cheese mixture to resealable bag and snip one of the corners. Pipe the filling into the manicotti shells and place in a single layer in prepared baking dish.
Top with remaining sauce (use more if you like it saucy) and remaining cup of mozzarella cheese. Bake for 25-30 minutes, or until sauce is bubbly.