Preheat oven to 375. Lightly grease an oblong shallow casserole dish (or similar).
To a mixing bowl, add the cooked squash "noodles," olive oil, garlic, basil, a generous amount of salt and pepper, and the parmesan cheese. Toss to coat (more olive oil can be added if needed - you want it moist, but not dripping). Spread mixture into the casserole dish. Lay tomato slices on top and season them lightly with salt and pepper. Sprinkle with mozzarella cheese and a little bit more freshly grated parmesan. Bake 25-30 minutes or until cheese is bubbly and beginning to brown. Serve promptly (a drizzle of balsamic and some more fresh basil on top is tasty, but optional).