When you have to register a refund or an amount you have returned because the customer has paid too much (or he did not receive the discount he was entitled to when paying in the first place) you basically follow the FAQ "How do I register a payment from a customer?". But when you enter the (negative) amount you enter a minus sign in front of it (i.e. '-219.50'). This will deduct the amount from what ever amount is outstanding in the invoice.