Heat a medium-size, heavy skillet over a medium flame. Add the ground beef and onion and sauté until the meat brown and the onion is translucent, about 5 minutes. Remove from the heat, and let cool slightly.
Meanwhile, in a medium bowl, mix the ricotta, 1 cup of the mozzarella cheese, ¼ cup of the Parmesan cheese, the parsley, garlic, salt, and pepper. Stir in the meat mixture and set aside.
Brush 1 teaspoon of the olive oil over a large baking sheet. Bring a large pot of salted water to a boil. Working in batches, add the manicotti and cook until softened but still firm to the bite, about 6 minutes. Using a slotted spoon, transfer the manicotti from the pot to the prepared baking sheet and let cool.
Preheat the oven to 350°F
Brush the remaining 2 teaspoons of oil over a 13x9x2-inch glass baking dish.
Spoon ½ cup of the marinara sauce over the bottom of the prepared dish. Fill the manicotti with the cheese-meat mixture, and arrange the stuffed pasta in a single layer in the prepared dish. Spoon the remaining cup of sauce over the manicotti. Sprinkle the remaining ½ cup of Parmesan cheese over the manicotti. Dot the top with the butter pieces. (The manicotti can be prepared up to this point 8 hours ahead. Cover and refrigerate.
Bake the manicotti uncovered until it is heated through and the sauce bubbles on the bottom of the dish, about 35 minutes. Let the manicotti stand for 5 minutes and serve.