Preheat oven to 425°.
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 tomatoes, thyme, oregano, basil, fennel seeds, Italian seasoning, parsley and bay leaves.
Bring to a boil, reduce heat, and simmer.
Mash up tomatoes with a potato masher until sauce is thickened , about 20 to 25 minutes. (Remove bay leaves).
Meanwhile, cook ravioli in a large pot of boiling salted water just until they float to the top (pasta will continue to cook in oven). (This will be about 3 minutes).
Drain pasta; return to pot.
Toss sauce with pasta.
Pour pasta into a 9-by-13-inch baking dish that has been sprayed with cooking spray.
Sprinkle with cheeses.
Bake until golden, 20 to 25 minutes.
Cool slightly before serving.