In a large saute pan, heat 2 Tbsp. of olive oil over medium high heat. Add the onions and saute until translucent, about 5 minutes. Add the bell peppers and saute for another 5 minutes. Add the garlic and cook 2 minutes more. Remove the onions, peppers, and garlic to a bowl.
Return the pan to the heat and add 2 more Tbsp of olive oil. Add the zucchini and yellow squash and cook until they are tender, about 5-7 minutes. Remove from the pan.
Return the pan to the heat and add the remaining 2 Tbsp of olive oil. Add the eggplant and saute for 2 minutes. Add the 1/4 cup of water; the eggplant will absorb all the oil very quickly and the water will help it cook before it burns. When the water is absorbed and the eggplant begins to soften (about 5 more minutes), add the chopped tomatoes to the eggplant.
Cook the tomatoes until they start to break down and the eggplant is soft, but not mushy. Add the onions, peppers, and squash back into the pan, folding it all together with a large spoon.
Cook for another 5 minutes and add the fresh herbs. Season with salt and pepper. Don't overcook; you want the flavors to remain fresh and distinct. Plus, if you reheat for later use, it's going to cook more then.