Heat the oven and boil the shells: Preheat the oven to 350°F. Boil the manicotti in a large pot of salted water for just 6 to 7 minutes, which is short of al dente on purpose so the tubes stay sturdy enough to stuff. Drain and lay them in a single layer on a lightly oiled sheet pan so they don't stick to each other.

Mix the cheese filling: In a large bowl, stir together the ricotta, 1 1/4 cups of the mozzarella, 1/2 cup of the parmesan, the egg, garlic, basil, 1 tablespoon of the parsley, nutmeg, salt, and pepper until smooth and evenly combined.

Season the sauce and start the pan: Stir the Italian seasoning into the marinara. Spread 1 cup of it across the bottom of a 9x13-inch baking dish so the tubes have something to sit in.

Pipe the filling: Spoon the cheese mixture into a gallon zip-top bag, press out the air, and snip 3/4 inch off one bottom corner. Pipe the filling into each tube from one end until it reaches the middle, then fill from the other end to meet it.

Assemble the dish: Arrange the filled tubes in a single layer over the sauce. Spoon the remaining 2 cups of marinara over the top, covering the ends of every tube so they don't dry out and turn leathery in the oven.

Bake covered: Cover the dish tightly with foil and bake for 30 minutes, until the sauce is bubbling around the edges of the pan.

Add the cheese and brown it: Uncover and sprinkle the remaining 3/4 cup mozzarella and 1/4 cup parmesan over the top. Return to the oven uncovered for 12 to 15 minutes, until the cheese is fully melted and golden in spots.

Rest and serve: Let the pan sit for 10 minutes before serving so the egg-set filling firms up and the tubes lift out whole instead of collapsing. Sprinkle with the remaining 1 tablespoon parsley.