my Cuinn who has been on phenobarb and potassium bromide for 2.5 years now has not exhibited the kinds of problems that you are talking about there have been other side effects but he has not regressed in housebreaking....
there is an excellent website for epi-dogs
http://www.canine-epilepsy.com/
there are a great many very knowledgeable folks on the listserve and the website itself has a wealth of information.... I would strongly encourage you to check it out....
I also commend you for learning about epilepsy in dogs and doing what is best for your guy.
S