Navigate to Money > Bank accounts.
Scroll to the bottom of the screen and click on the Explain link beside the appropriate bank statement to begin explaining.
Click on the appropriate receipt amount within the table of transactions to explain.
Select the appropriate customer in the From box.
A table with recent invoices for the customer will now appear. Use the box in the To pay off column to enter how much of the receipt to allocate to a particular invoice. By default, this will be the full amount.
Click on the Add transaction button to allocate the receipt to the invoice.