Preheat the oven to 375
Sautéed the onions with 1 Tbsp of the olive oil until soft, about 7-8 minutes. Add garlic during the last minute.
Spread mixture on the bottom of a baking dish.
Slice the zucchini, squash, eggplant, potatoes and tomatoes into 1/4 inch circles and layer them over the onions and garlic.
Drizzle 1 Tbsp olive oil on top, season with salt, pepper and fresh thyme.
Cover with foil and bake for 35 minutes.
Uncover, sprinkle cheese over the top and bake for another 30 minutes uncovered, until golden brown on top.