In a microwavable bowl, mix water and margarine (cut into pieces). Stir in stuffing mix and cover with a microwavable lid. Cook on HIGH for 8 to 10 minutes. Fluff with fork.
Place eggplant, zucchini, tomato, onion into a large skillet. Season with thyme, salt, and pepper. Cook and stir over medium low heat for 15 to 20 minutes. Remove from heat.
Preheat oven to 350 degrees F ( 175 degrees C). Grease a 2 quart casserole dish.
Layer vegetables, cheese, and stuffing in the dish until all ingredients have been used, ending with cheese.
