In a large saucepan, cover dried beans with triple their volume of cold water. Bring water to a boil over MEDIUM-High heat and cook beans, uncovered, for 2 minutes over medium heat. Remove pan from heat, cover, and soak beans for 1 hour.For alternative ways to soak beans, see NOTES below.
Drain and thoroughly rinse soaked beans.
If you are using a ham bone, put it in the slow cooker now.Combine presoaked beans with diced celery, grated carrot, and chopped onions in slow cooker. Add 1½-2 quarts of water + pan juices. (See NOTES for more about pan juices.)
Give everything in the slow cooker a quick stir. Add the crushed chili peppers at this time if you are using them. Set slow cooker to HIGH and cook for 5 hours. I usually stir the soup a couple of times during the cooking time.
After cooking for 5 hours, the meat on the ham-bone should be falling apart. Using tongs or an extra-large serving spoon, carefully remove ham bone to a plate and set aside to cool. Reduce the slow cooker to LOW. After you have removed the ham bone, taste the soup broth, and then season with salt and pepper to taste.
Add fresh thyme if desired. (Or any other fresh herbs you choose to use.) Allow soup to continue to simmer on low while ham bone cools, checking every 30 minutes until the beans are done to your liking. Beans are usually done in 6 to 8 hours. For a creamier bean soup, when the beans are fully cooked, use an emersion blender to blend some of the beans a bit. (Be sure to do this BEFORE you add any ham back into the soup.)
When the ham bone is cool enough to handle, separate the meat from the bone. Stir ham from bone into soup. Add any additional reserved ham at this time. Discard the ham bone and season to taste.
Ham bone: The type of ham bone you use will determine the underlying flavor profile of your soup. If you use a honey or glazed ham bone, your soup will be slightly sweeter. If you use a smoked hambone (or ham hock), your soup will taste more smokey.
Three Ways to Presoak Beans
Stovetop HOT Soak (Recommended): In a large saucepan, cover dried beans with triple their volume of cold water. Bring water to a boil and cook beans, uncovered, for 2 minutes over medium heat. Remove pan from heat, cover, and soak beans for 1 hour.
Instant Pot HOT Soak (Also good): I'm not a big Instant Pot user; however, when I do presoak my beans in my Instant Pot (and I have a couple of times) these are the directions I follow.
Countertop COLD Soak (Not recommended): Rinse the beans under cool, running water and remove any stones or shriveled beans. Transfer beans to a large bowl, and cover with enough water so that there is 2 inches of water above the beans. Let sit overnight. Drain and rinse thoroughly before cooking.
How to Use Pan Juices in Soup
If you are using pan juices (i.e.,ham juice from the bottom of the roasting pan):Refrigerate pan juices for at least four hours, until very cold. Using a sieve, strain the pan juices to filter out any fat solids and other bits you might not want in your soup.Use 16-24 ounces of pan juices in your soup; less if your ham was particularly salty or the juices very thick.Add enough water to the pan juices to make a total of 1½ to 2 quarts of liquid, depending upon how thick you like your soup. (i.e., more liquid = thinner soup) Add liquid to the ingredients in the slow cooker. If you DO use pan juices as part of your liquid: Hold off on adding any additional seasoning until after the first 4 hours.If you DO NOT use pan juices as part of your liquid: Add the brown sugar and black pepper at this time.DO NOT add any salt to your Navy Bean Soup at this time. Ham bones are notoriously salty, and it is easier to know how much salt to add once the ham bone has cooked out into the soup. As with most soups, Navy Bean Soup is always better the next day, when the flavors have had a chance to meld.