Preheat the oven to 350°F. Bring a large pot of salted water to a boil over medium-high. Boil the pasta until al dente, about 5 minutes. Drain and let cool for 10 minutes.
While the pasta is cooking, stir together the filling. In a large bowl, stir together the ricotta, eggs, 1 cup of mozzarella, ½ cup of parmesan, basil, Italian seasoning, salt, and pepper until well combined. Transfer the filling to a large ziptop bag or piping bag.
Lightly grease a 9x13-inch baking dish. Spread 1 cup of the marinara sauce evenly in the bottom of the baking dish. Cut a ½-inch hole in the corner of the bag with the ricotta filling. Stuff each manicotti with filling and arrange in a single layer in the baking dish. Spoon the remaining 2 cups of the marinara sauce over top of the stuffed pasta. Sprinkle with the remaining 1 cup of mozzarella and ½ cup of parmesan.
Bake until the sauce is bubbling and the cheese is melted, about 40 minutes. Turn the oven to broil and continue cooking until the top is lightly browned, 1 to 3 minutes. Garnish with basil.
