You'll want to apply credits through your connected accounting package. These will then sync through to Fergus and take payment off your selected customer invoice.
If you're not connected to an accounting package
You will need to re-issue your customer invoice. First, see this article on duplicating invoices. Once you've duplicated your invoice you'll want to add a line item with a negative dollar amount representing your credit:
You can call this line item whatever you like.
Do note that you cannot create an invoice with a negative Total.