Heat oven to 350 degrees F. Coat 13 x 9 x 2-inch baking dish with nonstick vegetable-oil cooking spray.
Combine beans, water, onion, bacon pieces, ketchup, molasses, brown sugar, mustard, salt, thyme, pepper sauce and black pepper in large bowl. Spoon bean mixture into prepared pan, spreading evenly. Arrange bacon strips over top. Cover dish with foil.
Bake in 350 degree oven for 3 1/2 hours. Let stand before serving until thickened, about 45 minutes. Makes 12 servings.