Rinse beans; place in a Dutch oven with 2 quarts of water. Bring to a boil; reduce heat and simmer for 3 minutes. Remove from heat and let stand for 1 hour. Drain and rinse. Return beans to Dutch oven with remaining water; bring to a boil. Reduce heat; simmer for 1 hour or until beans are tender. Drain, reserving cooking liquid. In the Dutch oven or 3-quart baking dish, combine beans, 1 cup cooking liquid, onion, ketchup, brown sugar, molasses, salt, mustard and bacon; mix well. Cover and bake at 350° for 2 to 2 1/2 hours or until beans are as thick as desired. Stir occasionally and add more of the reserved cooking liquid if needed.