Preheat an oven. Bring a large pot of water to a rapid boil, then season generously with a few tablespoons of Kosher salt. Cook the manicotti until very al dente. Drain or transfer with a slotted spoon to a bowl.
In a large mixing bowl, combine ricotta, shredded mozzarella, Pecorino Romano, eggs, garlic cloves. Chopped basil, Italian seasoning, Kosher salt, black pepper, and ground nutmeg. Stir until very well mixed.
Spread marinara sauce on the bottom of the baking dish. Next, fill the manicotti. Place the cheese mixture in a Ziploc bag, then cut off one corner. Arrange the stuffed manicotti in a single layer in the baking dish. Pour the remaining marinara sauce on top.
Sprinkle the remaining shredded mozzarella cheese and grated Pecorino evenly on top of sauce. Bake until the cheese is a light golden brown and the sauce is bubbly. Allow to cool before serving with additional fresh basil leaves!