As far as your 12.5v is concerned, that is the mid level charge in what is supposed to be a three charge system. 13.1v - boost phase, 13.5v 50-90% And float charge after that about 12.1v. However, if you have the stock WFCO charger - if Thor is still using them - Many have found that they do not charge at the boost level or float level or both. If you are down that far and only seeing 12.5v from your converter/charger then it is suspect.
For the water, I am with Bob. You are right that topping off the batteries should be done when they are fully charged, however, charging a dry battery can cause an explosion or fire, so I would put some water in them before charging. If the water has been below the plates, then the batteries may be toast anyway.
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