Melt margarine in a large ovenproof Dutch oven over medium heat. Add 1 cup onion and garlic, and sauté for 5 minutes. Add Marsala, parsley, 1/4 teaspoon thyme, 1/4 teaspoon pepper, 1/4 teaspoon salt, basil, and tomatoes; bring to a boil. Reduce heat; simmer, covered, 10 minutes. Spoon into a bowl; set aside.
Combine 1/4 teaspoon salt, 2 cups water, squash, and carrot in pan, and bring to a boil. Reduce heat, and simmer, partially covered, 30 minutes or until the vegetables are tender. Partially mash the beans with a potato masher, and add beans and tomato mixture to pan. Cook over medium-low heat 30 minutes or until thick. Remove from heat.
Preheat oven to 325°.
Rub chicken with 1/2 teaspoon thyme and 1/2 teaspoon pepper; set aside. Cook bacon in a large nonstick skillet over medium-high heat until crisp. Remove bacon from pan; crumble bacon, and set aside. Add chicken to bacon drippings in pan; cook 3 minutes on each side or until browned. Remove chicken from skillet; cut into 1-inch pieces. Add 1 cup onion and sausage to skillet; sauté 5 minutes or until lightly browned. Add the chicken, crumbled bacon, and sausage mixture to bean mixture in pan, stirring to combine.
Cover and bake at 325° for 1 hour. Uncover and bake an additional 30 minutes.