Chop tomatoes into approximately ½ chunks and place in strainer or colander to let drain over sink or bowl for at least half an hour
Slice eggplant and zucchini into ¼ to ½ inch slices and lay out on paper towels in a single layer - salt generously and let sit for at least half an hour
Chop up bell peppers into approximately ½ chunks and set aside
Slice onions and set aside
Create an herb bundle with the thyme, parsley, and half the basil (save the other half for later) by tying it with undyed string or thread
Once eggplant has released its liquid, press firmly with paper towels to remove as much liquid as possible
Pour ¼ cup olive oil into dutch oven or large saute pan and set over medium heat for 3 minutes
Add onions and saute for 3 minutes
Add eggplant to hot oil and saute for 3-4 minutes
Add remaining ¼ cup of olive oil
Next add zucchini and peppers and saute for another 3-4 minutes
Finally add the tomatoes and herb bundle and turn the heat down to medium-low and simmer for 20 minutes with no lid - stirring occasionally
Preheat oven to 350°
After vegetable have cooked on the stove top for 20 minutes remove herb bundle, place lid on dutch oven or transfer to oven safe pot with lid (if using a saute pan) and place in oven
Cook covered and undisturbed in oven for 40 minutes to allow flavors to meld and vegetables to become meltingly tender
Remove from oven and add remaining basil (stems removed and leaves torn in half)
Let cool slightly before serving and sprinkle with a pit of parmesan cheese if desired