If you're using the 'Receive Payments' function if there are no other outstanding amounts receivable for the customer the option to either 'Leave this as an underpayment' or to 'write off the extra amount will automatically appear.
If there are other amounts (invoices) receivable from this customer uncheck all of the invoices, and then re-cheque the invoice being paid. The same option should appear.
In case of overpayments the options will be to either 'Leave the credit to be used later' or 'Refund the amount to the customer'
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