Step 1: Cook the Pasta. Bring a large pot of salted water to a boil. Add the pasta and cook according to package directions until al dente. Drain well and set aside.
Step 2: Prepare the Sauce Base. While the pasta cooks, heat olive oil in a large skillet or Dutch oven over medium heat. Add the chopped onion and cook until softened, about 5-7 minutes. Add the minced garlic and cook for another minute until fragrant.
Step 3: Build the Sauce. Pour in the crushed tomatoes, tomato paste, Italian seasoning, red pepper flakes (if using), and sugar. Stir well and bring to a simmer. Reduce heat to low, cover, and let it cook for at least 15-20 minutes, allowing the flavors to meld. Season with salt and black pepper to taste.
Step 4: Combine Ingredients. In a large mixing bowl, combine the cooked pasta, the cottage cheese, 1 cup of the shredded mozzarella, and 1/4 cup of the grated Parmesan cheese. Pour in the prepared tomato sauce and mix gently until everything is evenly coated.
Step 5: Assemble and Bake. Preheat your oven to 375°F (190°C). Lightly grease a 9x13 inch baking dish. Pour the pasta mixture into the prepared baking dish, spreading it evenly. Top with the remaining 1 cup shredded mozzarella and 1/4 cup grated Parmesan cheese.
Step 6: Bake to Golden Perfection. Bake for 25-30 minutes, or until the cheese is melted, bubbly, and lightly golden brown on top. If desired, broil for the last 2-3 minutes for extra browning. Let the baked pasta rest for 5-10 minutes before serving. Garnish with fresh basil or parsley if using.