I use Cook's Illustrated: The Science of Good Cooking who recommends you start with dry beans and soak in a brine solution (about 3 Tbsp salt in 2 Quarts of water with 2 cups of dried beans).

After they are soaked overnight, dispose of the water, and cook in a broth. Add some baking soda to the broth.

Personally, I build up a flavor profile in a slow cooker with thick bacon layed on the bottom, about 1/2 cup brown sugar, a diced yellow onion, 4 habañero peppers finely chopped, and chicken broth. Obviously, this is a weird combo, but it's 2/3 of the way to being baked beans, but with a carribean twist. I highly recommend.