Preheat the oven to 350°F (175°C).
Bring a large pot of water to a boil, add a heaping pinch of salt, and cook the manicotti noodles until al dente according to package directions; drain and rinse under cold water to stop cooking.
In a mixing bowl, combine the ricotta, 1 cup of the mozzarella, 3/4 cup of the Parmesan, chopped parsley, chopped basil, beaten eggs, and black pepper until evenly mixed.
Spoon the cheese mixture into a piping bag or use a small spoon and carefully fill each manicotti shell with the ricotta mixture; place filled shells in a single layer in the prepared baking dish.
Spread 1 cup of marinara sauce across the bottom of the 9×13-inch baking dish before adding the filled shells, then arrange the shells on top.
Pour the remaining marinara sauce over the filled shells, then sprinkle with the remaining mozzarella and remaining Parmesan.
Cover the dish with foil and bake for 20–30 minutes, until heated through and the cheese is melted; remove foil and broil 1–2 minutes if you want the top browned.
Remove from the oven and let rest for 10 minutes, then garnish with additional parsley and basil before serving.