How to record allowing a tenant to pay in arrears?

Housing Benefit Overpayment

It is quite common to allow a housing benefit tenant to pay the rent at the end of each rental period even though the ast says that rent should be paid at the beginning of each rental period.

What I am wondering is what is the best way to record this so that everyone is clear what is happening and there is no bust up at the end of the tenancy with the landlord saying you need to pay for this last month and the tenant saying I have always paid up front so you have already had your money.

I am wary of putting anything in writing as it might be seen to create an alternative ast.

I have a situation where I made the tenant pay upfront for the first 6 months of a 12 month fixed term then let them begin the practice of paying in arrears. I did not put the arrangement in writing but I wrote a rent statement at the end of the first year showing the "arrears". 2 years later comes the bust up when the tenant swears blind that they have always paid up front. Obviously I can show the truth from bank statements but I am keen to avoid this sort of misunderstanding and conflict in the future.

What is good practice here?