Easy Baked Ziti

Name: Easy Baked Ziti
Ingredients: 1 medium yellow onion; 3 cloves garlic; 1 1/2 ounces Parmesan cheese (about 1/2 cup grated), divided; 2 tablespoons olive oil; 1/2 teaspoon red pepper flakes (optional); 5 cups marinara sauce (about 46 ounces); 1 1/4 teaspoons kosher salt, divided, plus more for seasoning; Freshly ground black pepper; 1 pound dried ziti or penne pasta; 1 cup whole-milk ricotta cheese; 8 ounces shredded low-moisture mozzarella cheese (about 2 cups), divided