To process a return on an invoice paid by integrated CC processing, simply go to Accounting>Invoices. Locate the invoice in question. Click the "Returns" Button.
The Return/Refund invoice will open. Any line items from that invoice that were paid will be showing. Each will have a Quantity of ZERO. Determine how much of what item you need to refund and modify the quantity (QTY) field.
In this example, there was only one bath charged. I'm refunding the entire bath so I change QTY from 0 to 1 (it'll change itself to a -1) and you can see the values adjust in the lower right. (If your charge had tax applied, it'll show in the refund as well.)
When it looks proper, click the "Issue Refund" button. It will open the "Refund" window. Choose your payment method. (In this case, we're applying it back to the CC.) Click either Process Now or if customer has CC on file they want to use, click "Retrieve Stored Credit Card" and then choose the card.
In the screen shot above we chose "Process Now" and the funds will go back to the card that was originally used.
Again, in KC you'll be prompted to print or cancel receipt if that option is enabled and the status will show "Approved".
The refund is now complete and you can close all windows.