Preheat oven to 350 degrees F.

Bring a large pot of salted water to a boil. Cook the ziti to al dente according to package directions. Drain without rinsing and return to the pot.

Heat olive oil in a large skillet over medium heat. Add the chopped onion and cook, stirring often, for about 2 minutes until softened.

Add the sausage to the skillet. Crumble and cook until browned, about 5 minutes. Add the minced garlic and stir for 30 seconds until fragrant.

Add the marinara sauce, Italian seasoning, dried basil, black pepper, and red pepper flakes if using. Stir to combine, bring to a simmer, reduce heat, and cook for 10 to 15 minutes.

Remove skillet from heat. Spoon 1 cup of the meat sauce into the bottom of a 13x9-inch baking dish and spread evenly. Stir two-thirds of the remaining sauce into the drained pasta. Transfer half of the saucy pasta to the baking dish and spread into an even layer.

Dollop spoonfuls of ricotta over the pasta layer. Sprinkle one-third of the mozzarella and 0.25 cup of the Parmesan on top. Add the remaining pasta in an even layer. Top with the remaining meat sauce, mozzarella, and Parmesan.

Spray one side of a sheet of foil with cooking spray and cover the baking dish with the sprayed side facing down to prevent sticking. Bake covered for 35 minutes. Uncover and bake for 10 to 15 more minutes until hot, bubbly, and the cheese on top is golden brown. Total bake time is 45 to 50 minutes.

Let the baked ziti rest for 10 minutes before serving so the layers set and it scoops cleanly.