If the remaining balance of an invoice, needs to be credited then you can do so by using the options under the Payment history table. The system will create and apply a credit note with the same details as the invoice.
Navigate to Sales > Invoices > Unpaid.
Click on the appropriate invoice number that you would like credited from the list.
When viewing the invoice to be credited, scroll down to the bottom of the invoice and click on the 'Credit' tab to the right of the 'Payment history' section.
This will bring up a form giving the option to credit the outstanding balance on the invoice at the click of a button.
Click the apply 'Apply credit note' button and the system will automatically create a credit note and apply it against the outstanding balance of the invoice in question.