To make the sauce, sautee the onion, 4 cloves garlic, red and yellow bell pepper and a teaspoon of salt in the 3 tablespoons olive oil until the vegetables start to soften. Finely chop the 8-10 basil leaves and add to the sauce off heat. Stir in crushed tomatoes and season with additional salt and pepper to taste. Transfer to an oven-safe dish and smooth with a spatula.
Slice the eggplant, squashes, and tomatoes very thinly, no thicker than 1/4". Layer in alternating pattern and nestle edge-down in sauce. Cover dish tightly with foil and bake in 375 degree oven for 40 minutes. Remove foil and bake an additional 20-30 minutes, until vegetables soften.
To make herb drizzle, combine additional 8-10 leaves basil, oregano or thyme leaves, parsley, 2-3 cloves garlic, and 6 tablespoons olive oil in food processor. Pulse until herbs and garlic are finely minced. Season with salt and pepper to taste, and drizzle over vegetables as soon as they come out of the oven.