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Line a large platter with paper towels. Heat ½ cup olive oil in a medium saucepan over medium heat. Add the eggplant, season generously with salt and pepper, and let that cook down for 10 to 12 minutes, until the eggplant is soft and wilted. With a slotted spoon, remove the eggplant from the pan and onto the paper-towel-lined platter to drain.
Next, cook the zucchini and yellow squash the same way, adding another ½ cup oil if necessary. Add it to the platter with the eggplant.
Add another ½ cup olive oil to the pan, then the anchovies, onions, garlic, and herbs. Cook for 5 to 7 minutes, until the onions get nice and caramelized.
Add the tomatoes and cook that down for 10 to 12 minutes, until pulpy. Return the eggplant and zucchini to the pan, crack open the chile, and add that too. Season with salt and pepper and let the ratatouille cook slowly for about 20 minutes until the mixture is soft, mushy, and juicy; you want all the flavors to come together.
Stir in the vinegar and let cool to room temperature.