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.

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.