Step 1Heat the oven to 450 degrees. Coat the peppers with a thin film of olive oil (about 2 tablespoons), then place the peppers, flesh side down, on a foil-lined baking sheet. Roast until the skin begins to loosen, then remove from the oven, 10 to 15 minutes. Transfer the peppers to a plastic bag, and set aside to steam until they are cool enough to handle. Peel the peppers. (As an alternative to roasting the peppers, you can use a blowtorch to char the skins of the peppers while they are still whole, and then gently scrub the charred skin off under running water to remove the skins.) Dice the peeled peppers into one-half-inch pieces and set aside. Reduce the oven temperature to 350 degrees.
Step 2Bring a small pot of water to a rapid boil. Stem the tomatoes and score the skin on the bottom into an X. Plunge one tomato at a time in the boiling water until the skin begins to loosen, about 15 seconds. Immediately transfer the tomato to a bowl of ice water to stop the cooking. Repeat this process with the remaining tomatoes. Remove the tomatoes from the ice water and peel the tomatoes. Dice the tomatoes into one-half-inch pieces, saving all the juice, then set them aside.
Step 3Cut the thyme sprigs, parsley sprigs and bay leaves into approximately 1-inch lengths. Place the herbs in the center of an 8-inch-square piece of cheesecloth. Gather the ends of the cheesecloth around the herbs, and twist them to form the herbs into a sachet. Tie the sachet securely with a piece of butcher's twine.
Step 4Heat a wide, shallow pot or roasting pan over medium heat and add one-half cup oil. Add the onions and the sachet of herbs to the pot along with a good pinch of salt — this will help release the liquid inside the onions and allow them to sweat without coloring. Sweat the onions until they are soft and translucent, about 10 minutes. Add the garlic and sweat until it is fragrant and the raw flavor has subsided, about 2 minutes.
Step 5Add the tomatoes and peppers to the pot along with another pinch of salt, and bring them to a gentle simmer. The tomatoes will begin to release their liquid. Use a rubber spatula to scrape the sides of the pot clean.
Step 6Place the cartouche or paper lid on top of the surface of the tomatoes, taking care to press out the air pockets and transfer the pot to the center rack of the oven. Bake the ratatouille base in the oven, periodically removing the pot from the oven and giving it a stir. Continue to bake until almost all of the liquid has evaporated but the tomatoes are still moist, 1 to 11/2 hours. If needed, remove the cartouche toward the end of baking to help the liquid reduce more quickly.
Step 7While the ratatouille base is baking, heat a large sauté pan over medium-high heat. Add approximately one-half cup oil and the yellow zucchini (the zucchini should cover the pan in a single layer; if necessary, cook the zucchini in batches). Lightly season the zucchini with salt and pepper, and cook until the zucchini is lightly caramelized and just barely cooked through, 6 to 10 minutes per batch. Transfer the cooked zucchini to a baking sheet, then repeat this process with the green zucchini and then the eggplant, adding more oil each time (you will use approximately one-half cup oil for each of the vegetables).
Step 8Once all of the vegetables have been cooked, remove the cartouche from the ratatouille base and fold the zucchinis and eggplant, their juices and oil, into the base. Stir to incorporate all ingredients evenly, then clean the sides of the pot with a rubber spatula, re-cover with the cartouche and return the pot to the oven. Bake until the vegetables are very tender and the ratatouille thickens, 45 minutes to an hour.
Step 9Adjust the seasoning with salt, freshly ground pepper and a couple of drops of balsamic vinegar. You can either serve the ratatouille right away or let it sit overnight and let the flavors further meld. Serve the ratatouille as a side dish to seafood, poultry or meat.