Preheat the oven to 350 F°.
In a large bowl, combine the ricotta, spinach, onion, egg, garlic, Italian seasoning, nutmeg, salt, pepper, 1 cup of the mozzarella cheese and 1/2 cup of the Parmesan cheese.
Spread about 1 cup of the marinara sauce in the bottom of a 9x13-inch casserole dish. Transfer the filling to a piping bag or plastic ziploc bag, cut off a little from one end, this will make it easier for stuffing the shells.
Stuff each manicotti shell with ricotta mixture and arrange in a single layer in the dish. Cover with remaining sauce. There should be enough sauce to fully cover the manicotti.
Top with remaining 1 cup of mozzarella cheese and 1/2 cup of Parmesan cheese.
Transfer the dish to the preheated oven and bake for 1 hour covered, then 15-20 minutes uncovered, or until the noodles are soft.
Serve garnished with basil if preferred and more grated Parmesan cheese.