The recipe starts out by cooking the (pre-soaked) beans in a slow-cooker for three hours. The beans are then drained and added back to the slow-cooker -- along with smoked paprika, dried mustard, grated onion, molasses, brown sugar, ketchup, and water -- to cook for another 10 to 14 hours. I let mine simmer overnight on low heat. While I was sleeping, the beans transformed from pale to tangy brown.
Recipe here. I used cannellini instead of navy beans, and added salt to the cooked beans.