Preheat the oven to 375 degrees. Spray a 9-inch round or oval baking dish with non-stick cooking spray.
Heat 1 tablespoon olive oil in a large skillet over medium heat. Add the onions and sauté until translucent, about 5-7 minutes. Add the garlic and cook for another minute. Spread the onion mixture on the bottom of the prepared baking dish.
Slice the potatoes, zucchini, squash and tomatoes into 1/4 inch thick slices. (I like to use a mandolin for slicing the vegetables.) Layer them alternately in the dish on top of the onions, fitting them tightly into a spiral, making only one layer. Season with sea salt, black pepper and dried thyme, to taste. Drizzle one tablespoon of olive oil over the top.
Cover the dish with foil and bake for 30-35 minutes, or until the potatoes are tender. Remove the foil and sprinkle the Parmesan cheese and bake for another 15-20 minutes or until golden brown.