When customers receive a payment receipt email, they will see the invoice numbers that their payment was applied to.
When you send a payment receipt email to a customer (via Accounts Payable > Deposits > payment on a deposit > More buttonDeliver), the email lists any invoices that the payment was applied to. This applies to both CC/eCheck and manual payments. For example:
If no invoices were applied, the email message tells the customer the payment has not been applied to an invoice:
