The second payment can be allocated to Accounts Receivable then select the customer name without the optional invoice number. This will result in a credit balance in the customers account. When you issue the next invoice, Manager will automatically allocate the credit balance to that invoice. Credit notes are not applicable to accounts overpaid by customers, see guides - https://forum.manager.io/t/credit-notes-for-customer-returns-and-refunds/7425.
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