The liquid left over from cooking your beans is essentially bean broth. It's full of flavor. I like to save it and use it to fortify other dishes.
2 cups dry beans
1 onion, peeled and cut in half
1 bay leaf
1 teaspoons salt
Place your beans in a medium sized heavy pot and cover with 10 cups of water. Bring to a boil and then lower the heat to medium. Add the onion, bay leaf and salt. Salting beans early on in the cooking process is controversial. If you prefer to add the salt later do that, but I've never had any problems salting my beans early and find they taste better when I do.
Cook your beans at a gentle simmer for about two hours. Checking on them every once in a while to make sure the liquid has not completely evaporated. Add more if it has. You want your beans to have about 1-2 inches of water above them at all times. While you are checking on them gently stir them so they cook evenly.
Start checking your beans after 1 1/2 hours have passed. I like to nibble on one as a test. The beans are ready when they are completely soft and creamy. When they are cooked through turn off the heat and allow them to cool a bit. Strain the beans and reserve the cooking liquid.