Soak beans: Place dried beans in a large saucepan or Dutch oven. Add enough cold water to cover the beans. Stir, cover the pan. Let stand at room temperature at least 8 hours or overnight. Drain water and rinse beans, drain again.
Make Beans: In a large soup pot, combine 6 cups of water and soaked beans. Bring to a boil. Lower the heat and simmer, uncovered 2 hours or until beans are tender. Drain beans, reserving 1/2 cup liquid.
Preheat oven to 325º
In a 2-quart casserole or bean pot, combine cooked beans, onion and bacon or ham. Stir in 1/2 cup apple cider, brown sugar, molasses, ketchup, dry mustard, salt and pepper.
Bake, covered, for 2 to 2-1/2 hours or until desired consistency, stirring occasionally, adding more apple cider if needed.