Hi Tracey
If you created an "Invoice" for this Customer, you need to enter the payment via "Receive Payment". This window will show all outstanding invoices to which you can apply their payment accordingly. You can then choose to move this payment ("Deposit to") either to your "Undeposited Funds" account (if it's Cash or a Cheque to be deposited) or directly into your Bank Account (if paid to you by EFT)
Sales Receipts are for "Cash Sales" or where the customer pays at the time of the sale, as opposed to Invoices which are used for customers who pay later.
Hope that clarifies ...