Does anyone know if there is a way to set up budgets for a restaurant that work on 13 period instead of month? We were told that Quickbooks can do this but we have not been able to find out how to make it work?

I don't know who told you this because QB does not have this capability. Get them to set it up for you. Whatever it is will be a real workaround, you can bet on it. Take a look at the budget screen. There is no way to tell it not to use a full month.