Bodacious,
When you say "from scratch", do you mean dried beans? If so, you won't get them tender enough from start to finish, in a smoker. At least I can't, even after soaking them overnight. What I do is soak them overnight, (any bean will do here) cover them with fresh water (unsalted) and bring them to a boil. Simmer for 45 minutes, remove from heat and let them steep for 30 minutes.
Drain the beans, reserving the liquid, and combine them with your favorite ingredients. Place all in a roasting pan and set on the lowest rack of your smoker.
Set your meat over the bean pan and smoke away. If the beans require more moisture through the smoking process, add back some bean broth.