Bring a large stockpot of generously salted water to a rolling boil. Add the 14 manicotti shells and stir gently right after adding them so they don't stick together.
Cook the shells for 1 to 2 minutes less than the package instructions suggest for al dente, since they'll finish cooking in the oven. Drain and rinse under cool water, then lay out in a single layer on a baking sheet or clean kitchen towel.
Preheat your oven to 375 degrees Fahrenheit. In a large mixing bowl, combine the ricotta cheese, 1 1/2 cups of the mozzarella cheese, and the parmesan cheese.
Add the 2 eggs, minced garlic, chopped parsley, chopped basil, Italian seasoning, salt, pepper, and nutmeg. Stir everything together until the mixture is smooth and evenly combined, with no streaks of egg remaining.
Cover the bowl and refrigerate the filling for 10 minutes if your kitchen is warm, since a slightly chilled filling is easier to pipe.
Spoon the cheese filling into a piping bag or a large zip top bag with one corner snipped off. Pipe the filling into one end of a cooked shell, then turn the shell around and pipe from the other end to fill it completely.
Repeat with the remaining shells until all 14 are filled and set aside on a plate or tray. Work gently, since boiled pasta tears more easily than you might expect.
Spread 1 cup of the marinara sauce evenly across the bottom of your 9x13 inch baking dish. Arrange the filled manicotti shells in a single layer over the sauce, seam side down.
Pour the remaining 2 cups of marinara sauce evenly over the top of the shells, making sure each one is covered. Sprinkle the remaining 1/2 cup of mozzarella cheese over the top, along with a little extra parmesan if you'd like.
Cover the baking dish tightly with aluminum foil to keep the shells from drying out. Bake for 25 minutes covered, then remove the foil.
Bake uncovered for an additional 10 to 15 minutes, until the cheese is melted and just starting to turn golden in spots. The sauce should be bubbling gently around the edges of the dish when it's done.
Let the manicotti rest for 5 to 10 minutes before serving so the filling has time to set slightly. Sprinkle with a little extra chopped parsley or basil right before serving for a fresh finish.