Preheat the oven to 375 degrees. Spray a square or round baking dish with cooking spray.
Heat 1 tbsp of olive oil in a large skillet over medium heat, add the onions and saute until translucent, about 8 minutes.
Add the garlic and cook for another 60 seconds, watching as not to burn the garlic. Spread the onion and garlic mixture on the bottom of the greased baking dish.
Slice the potatoes, zucchini, squash and tomatoes in 1/4 inch thick slices.
Layer them alternately in the dish on top of the onions, fitting them into tight rows (for the square pan)or into a spiral (if using a round dish) leaving a small amount of wiggle room, making only one layer.
Season with sea salt, black pepper and dried thyme, to taste and drizzle the last tablespoon of olive oil over the top. Add an extra tablespoon if you needed.
Cover the dish with tin foil and bake for 40 minutes, or until the potatoes are tender. Uncover and sprinkle the Parmesan cheese on top and bake for another 25-30 minutes or until browned.