1. Preheat oven to 425 degrees. Heat oil in a large saucepan over medium heat. Add onion and garlic, and season with salt and pepper; cook, stirring occasionally, until softened (about 5 minutes). Add thyme and tomatoes. Bring to a boil, reduce heat, and simmer, breaking up tomatoes with a spoon, until sauce is thickened and reduced to about 5 1/2 cups, 20 to 25 minutes.
2. Meanwhile, cook ravioli in a large pot of boiling salted water just until they float to the top (the pasta will continue to cook in the oven). Drain pasta; return to pot.
3. Toss sauce with pasta. Pour pasta into a 9 x 13 baking dish, and sprinkle with cheeses. Bake until golden, 20 to 25 minutes. Cool slightly before serving.