I almost always add a little extra boiling water at a few points during the cooking time if the sauce thickens too quickly before the beans are fully cooked, usually about 1 to 1½ cups at a time. This is not a problem at all and is to be expected.
The cooking time seems to vary a great deal depending upon the type of white bean you are using. I have seen some that can take up to 8 hours to fully cook in a slow oven. The best approach is to consider this an all day recipe that you start in the morning for dinner. Baked beans are even better when cooked a day ahead, which is how I mostly cook them.