Prepare the sauce
In a large pot, sweat the onions in the olive oil over medium heat until clear. Add the garlic and thyme. Cook for another minute.
Add the tomatoes, sauce, and paste. Stir to combine.
Reduce temperature to simmer and continue to cook uncovered, stirring often, for an hour. Season with salt and pepper to taste.
Prepare the rigatoni noodles.
Bring 6 quarts of water to a boil over high heat.
Once boiling, salt the water and add the noodles. Stir to separate any clumps.
Reduce heat to medium and cook the rigatoni noodles according to package directions, minus 2-3 minutes.
When cooked to "al dente," drain the noodles but do not rinse.
Assemble the casserole
Preheat the oven to 375F.
In a large bowl, combine the noodles, sauce, and 3/4 of the cheese.
Spread into a casserole dish.
Top with remaining cheese.
Bake at 375F for 20-30 minutes or until bubbly and the cheese is melted.
Serve warm!