Preheat the oven to 375°F and lightly grease a 9x13 baking dish.
Bring a large pot of salted water to a boil and cook the ziti according to package directions until just al dente. Drain and set aside.
Heat the olive oil in a large skillet over medium heat. Add the diced onion and cook for 3 minutes until softened.
Add the ground beef to the skillet and cook until browned, breaking it up with a spoon. Stir in the minced garlic, salt, and black pepper and cook for 1 minute more.
Pour the marinara sauce into the skillet with the meat mixture and simmer for 5 minutes, then remove from heat.
In a mixing bowl, combine the ricotta cheese with 1 cup of the mozzarella and 1/4 cup of the Parmesan.
Spread a thin layer of meat sauce in the bottom of the prepared baking dish. Add half the cooked ziti, then dollop and spread the ricotta mixture over the pasta. Top with half the remaining meat sauce.
Add the rest of the ziti, the remaining meat sauce, and finish with the remaining mozzarella and Parmesan.
Bake uncovered for 25 minutes until the cheese is melted and the edges are bubbly. Let rest for 5 minutes before serving.