Preheat Oven : Preheat your oven to 375°F (190°C).
Prepare Marinara Sauce : Heat olive oil in a skillet over medium heat. Sauté chopped onion until translucent, then add minced garlic for 1 minute. Add marinara sauce, dried basil, red pepper flakes, salt, and pepper. Simmer for 10 minutes, stirring occasionally.
Cook Pasta : Cook manicotti pasta tubes according to package directions until al dente. Drain and rinse with cold water to prevent sticking.
Prepare Cheese Filling : In a bowl, combine ricotta, mozzarella, Parmesan, egg, garlic powder, dried Italian herbs, salt, and pepper. Mix until smooth and well combined.
Stuff the Manicotti : Use a spoon or piping bag to fill each manicotti tube with the cheese mixture.
Assemble in Baking Dish : Spread ½ cup of marinara sauce on the bottom of a 9x13-inch baking dish. Arrange filled manicotti in the dish in a single layer. Pour remaining sauce over the manicotti, ensuring they are well covered. Sprinkle shredded mozzarella and Parmesan on top.
Bake : Cover dish with aluminum foil and bake 30 minutes. Remove foil and bake an additional 10 minutes until cheese is golden and bubbly.
Serve : Garnish with fresh basil or parsley. Serve hot with garlic bread or a side salad.