Preheat the oven to 375°F (190°C).
Cook the penne pasta in a large pot of salted boiling water until al dente, about 9 minutes. Drain and set aside.
Heat olive oil in a large skillet over medium heat. Add diced onion and cook until translucent, about 5 minutes.
Add minced garlic to the skillet and cook for 1 minute until fragrant.
Add ground beef to the skillet and cook until browned, breaking it up with a spoon, about 7 minutes. Drain excess fat if necessary.
Stir in marinara sauce, dried oregano, dried basil, salt, black pepper, and red pepper flakes. Simmer for 10 minutes to blend flavors.
In a large mixing bowl, combine cooked pasta, meat sauce, and ricotta cheese. Mix well.
Transfer half of the pasta mixture into a 9×13 inch baking dish. Sprinkle half of the shredded mozzarella and half of the grated Parmesan over the pasta.
Add the remaining pasta mixture on top and spread evenly. Sprinkle the remaining mozzarella and Parmesan cheese on top.
Cover the baking dish tightly with aluminum foil.
To freeze: Place the covered dish in the freezer for up to 3 months.
To bake from frozen: Preheat oven to 375°F (190°C). Remove foil and cover with fresh foil. Bake covered for 45 minutes, then uncover and bake an additional 10-15 minutes until cheese is bubbly and golden.
Garnish with chopped fresh parsley before serving.