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 al dente according to package directions; drain and rinse with cold water to stop cooking.
In a medium bowl, combine the ricotta, 1 cup of the mozzarella, ¾ cup of the parmesan, chopped parsley, chopped basil, beaten eggs, and black pepper; stir until well mixed.
Spread 1 cup of marinara sauce in the bottom of a 9×13-inch baking dish.
Transfer the ricotta mixture to a piping bag or use a spoon to fill each manicotti shell; place filled shells seam-side down in the prepared baking dish in a single layer.
Pour the remaining marinara sauce over the shells, then sprinkle with the remaining mozzarella and parmesan cheeses.
Cover the dish with foil and bake for 20–30 minutes until heated through and cheese is melted; if desired, broil 1–2 minutes at the end to brown the top.
Remove from the oven and let rest for 10 minutes, then garnish with additional parsley and basil and serve.