Add 1 tablespoon of oil in a medium Dutch oven over medium heat. Once the oil is hot, add the zucchini and squash. Sprinkle with a pinch of salt and pepper.
Sauté the vegetables until beginning to soften and brown lightly, approximately 7 to 10 minutes. Remove the vegetables to a bowl and set aside.
Maintaining medium heat, add another tablespoon of oil. Once hot, add the onion and bell peppers. Season with a pinch of salt and pepper.
Sauté the vegetables until beginning to soften and brown lightly, approximately 7 to 10 minutes. Remove the vegetables to a bowl, and set aside.
Add another tablespoon of oil to the pan over medium heat. Add the eggplant and sauté until just softening. Add a pinch of salt and pepper and continue to cook, stirring often, until the eggplant is browning and the skins are becoming tender, approximately 10 to 15 minutes.
Preheat the oven to 350 degrees.
Add the tomatoes, garlic, oregano, thyme, and rosemary. Add all the other vegetables back to the pan, and gently stir to combine. Taste for seasoning and add salt and pepper as necessary.
Lower the heat and simmer until the oven is ready.
Place the lid ajar on the Dutch oven and place in the oven for 20 to 30 minutes or until the vegetables are further softened and tomatoes are completely soft.
Remove the pot from the oven and remove and discard the herbs.
Drizzle any desired oil over the Ratatouille. Serve very warm.