Bring a large pot of salted water to a boil. Add in the manicotti and cook for 7 minutes. Drain.
Set aside the pasta to cool and begin making the filling.
In a large bowl, mix together the Ricotta cheese, 3 ounces of Mozzarella, 3 ounces of Parmesan, cream cheese, Italian seasoning, and basil.
Heat the olive oil in a small skillet over medium heat. Add the spinach, onion, and garlic and cook until the onion is translucent and the spinach has wilted, about 5 minutes.
Add the spinach to the cheese mixture and stir well to combine.
When the pasta is cool enough to handle, use a small spoon to scoop the filling into the pasta. Alternately, place the filling in a plastic bag and snip off the end. Squirt the filling into the manicotti.
Cover the bottom of a 9x13 baking dish with a thin layer of marinara sauce. Arrange your pasta in the baking dish. Cover with the remaining marinara sauce and top with the remaining cheese.
Bake in a preheated 350 degree oven for about 20 minutes or until the cheese is melted and starting to browned on top. Sprinkle with parsley before serving.
For the sauce:
Heat the oil in a large sauce pan over medium heat. Add the onion and garlic and saute until soft and fragrant, about 5 minutes.
Add the remaining ingredients, stir to combine, and simmer for 30 minutes over low heat, stirring occasionally.
Store sauce tightly covered in the refrigerator for up to 5 days.