Preheat the oven to 500 degrees F. Place foil tightly over a baking sheet and spray with the nonstick spray. Place the eggplant in single layers on the baking sheet.
Lightly cover the eggplant with 1 tablespoon of olive oil and bake for 5 minutes. Turn the eggplant over and cook for another 5 minutes. Decrease the temperature of the oven to 350 degrees F.
Place a medium saucepan over medium-high heat and put 1 tablespoon of olive oil, garlic, and onions in the saucepan and sauté for approximately 5 minutes, or until the onions are tender. Pour in the tomato sauce, tomatoes, red pepper flakes, oregano, basil, and thyme. Reduce the heat to medium-low and simmer for another 30 minutes. Sprinkle salt and pepper for taste.
Take an 8X8 inch lasagna pan and pour in enough sauce to cover the bottom of the pan then arrange the eggplant on top. Sprinkle the ricotta cheese over the eggplant and coat with more sauce. Continue the same process two additional times so that you have a total of three layers and you end with sauce on top.
Sprinkle the mozzarella cheese over the top and spread the Parmesan cheese over the top of the entire dish. Put the pan in the oven and bake for 35 minutes.