Add the tomato product you have chosen to use (I used ketchup), the Guinness, vinegar, molasses, mustard, beans and a generous amount of salt and pepper. Bring the mixture to a simmer. Stir in the quartered onion and the chopped apple. Cover the pan and put it in the oven to bake for at least one hour. I baked my beans for several hours, adding additional liquid to keep the beans moist. I used the extra Guinness, but you could also use apple juice.I turned down the oven heat to 300 degrees F. after the first hour of baking. You will want to bake your beans until the sauce on the beans is thick and bubbling.