Open a customer account for the debtor.
Use the customers>receive payments option to capture the payment received.

As you have not generated an invoice as yet, the customer's account will be in credit.

Now, when you are ready, you can generate an invoice in the normal fashion. However, the payment received won't be linked to the invoice as yet.

Run the receive payments option again - you will see the invoice and there will be a credit to allocate.
Select the invoice that needs the payment matched to it by clicking anywhere in that line.
Click the set credits button below the list of invoices, allocate the credit against the invoice, and save. Basically you are saving a nil payment transaction, but it matches up the payment and invoice, thus clearing the transaction from the open invoices list.