I have always done this in a special book that details these things. It covers every time I have had to speak to them and is all in one place. They really don't like it when you ask for a reference number, but they have to give you one.
The businesses will tell you that it's the banks fault that they have to charge their customers for using electronic payments. It is a fact that any bank fees charged to the business are all tax deductible. Therefore, there is no need to charge their customers to use these methods of payments...