This master recipe is from Steve Sando at Rancho Gordo - he knows beans better than anyone on the planet, so who're we to tell you how to cook 'em!
Take it away, Steve!
"There is not one single method of cooking beans. At its most basic, you want to simmer the pot until the beans are soft. Soaking can speed up the process and vegetables or stock will make them more flavorful. It's really that simple."
Normally on a bean cooking day (which frankly is everyday at Rancho Gordo), I put the beans to soak in the morning, after rinsing in lots of cool water and checking for small debris. I cover the beans by about an inch or so. If you haven't soaked, don't fret. Go ahead and cook them, knowing it will take a bit longer.
Heirloom and Heritage varieties don't need a lot of fussing if they are used fresh, which I'd define as within two years. You can use a ham bone, chicken stock or as I prefer, simply a few savory vegetables.
A classic mirepoix is a mix of onion, celery and carrot diced fine and sautéed in some kind of fat, often olive oil. A crushed clove of garlic doesn't hurt. If I'm cooking Mexican or Southwestern, I will sauté just onion and garlic in mild bacon drippings or even freshly rendered lard.
Add the beans and their soaking water to a large pot. You have been told before to change the water and rinse the beans. The thinking now is that vitamins and flavor can leech out of the beans into the soaking water you are throwing down the sink. There is no scientific evidence that changing the water cuts down on the gas.
The beans will have expanded, so make sure they are still covered by at least an inch, maybe a bit more. Add the sautéed vegetables and give a good stir. Raise your heat to medium high and bring to a hard boil.
Keep the beans at a boil for about five minutes and then reduce them to a gentle simmer, then cover. I like to see how low I can go and still get the occasional simmering bubble. When the beans are almost ready, the aroma will be heady. They won't smell so much like the vegetables you've cooked but the beans themselves. At this point. I'd go ahead and salt them. Go easy as it takes awhile for the beans to absorb the salt. If you want to add tomatoes or acids like lime or vinegar, wait until the beans are cooked through.
If the bean water starts to get low, always add hot water from a tea kettle.
So you're done! Once you've mastered this method, go ahead and try some different techniques. Your bean friends will swear by this or that method and you should take their advice, keeping in mind there are few absolutes when it comes to cooking beans, only that is very hard work to mess up a pot of beans.