This is our first year storing a Class A for the winter. Previously, with towables (and inexpensive used ones, at that), I just protected the plumbing and not much else. Now, with a brand new Class A,...
Personally, I would make sure they are fully charged and then remove them. It will take less time than you will spend returning to the RV every couple of weeks to run the generator and it will make your life pretty easy. They don't need to be put on a charger at home, just keep them in a space where they won't freeze. Reverse the process in the Spring and you are ready to travel.