My experience with cooking something for so long is that the water level goes way down...so if that happens, is it OK to add more water? You say to fill the pot with trimmings up to 2 inches from the top...then add water, and the water should also not go over 2 inches from the top. This would not be much water... for me, at any rate, I would end up boiling the pot dry long before 3-4 hours, even at just a strong simmer.
Many a bean, at my house, has met with such a fate....
If so, how much water to add and how often, as not to dilute it too much?