Place beans in a large heavy pot, cover beans with 6 cups fresh, cold water. Heat to boiling. Skim. Turn heat down and simmer 1 hour. Drain beans, reserving 2 cups of the cooking liquid.
In heavy skillet, cook bacon. Drain and reserve fat. Remove bacon to a paper towel lined plate to drain.
Add chopped onion to skillet with 1 Tbsp reserved bacon fat. Cook until soft, adding a little water as needed to soften/cook onions without browning them.