You don't really say where you fit into this picture. Are you the Office Manager that will be using the QuickBooks system and do you know how to use it? If not, then they seem to have the whole situation under control they way it is. The accountant is keeping the books on QuickBooks already and entering the transactions the way they work for him when preparing the taxes so he doesn't have to fix the books later. That should be a savings right there. I'm sure that if the owner wanted statements, the accountant could pop them right out for him.
"If it's not broke, don't fix it."