Preheat oven to 350 degrees and grease a 2 qt. casserole dish.
In a large sauce pan, brown the ground beef and chopped onion.
Once browned, add the pasta sauce and bring to a boil. Reduce heat and let simmer.
Bring a large pot of salted water to a boil. Cook pasta according to package directions, subtracting 2 minutes.
Once pasta is cooked, reserve 1/2 cup of cooking water and drain additional water.
Slowly mix milk, pasta water, and 1/4 cup parmesan cheese into the sauce. Add pasta and mix again.
Pour 1/2 of the pasta and sauce into the greased casserole dish. Top with 1 cup mozzarella, 1/2 cup cheddar cheese, and 1/4 cup parmesan cheese.
Pour the rest of the pasta and sauce into the dish and top with remaining cheese.
Bake uncovered for 30 minutes, or until cheese is melted and sauce is bubbling.