If you want to create a credit note on one of your issued invoices that is yet to be paid, simply navigate to the "Sales" tab and then to "Invoices" in the sub menu to see a list of your invoices:
Then navigate to the "Options" menu of the relevant invoice and select "Raise credit note":
Clicking on "Raise credit note" will then display that a draft credit note has been created and on the invoice's line you'll see some blue writing under "Credit notes" referring to the amount and number of credit notes on this invoice:
To issue the credit note, click that blue writing to be taken to the "Invoice Summary" page. Here you can click the "Options" button next to the relevant credit note at the bottom of the screen and select "Issue":
You'll now see that the overdue amount of your invoice has been reduced by the credit noted amount.