To issue a full refund via the API, you simply need to make a /checkout/refund call and pass in the checkout_id and refund_reason.
Alternatively, if you login to the WePay App Center as the administrator of an account, you can issue a refund by clicking on a checkout in the transaction log and clicking the blue "Refund" button.
You can issue a partial refund by making a /checkout/refund call and passing in the optional amount and app_fee parameters. The amount specifies the total amount refunded to the payer, and the app_fee specifies the portion of the amount that will be refunded by the application.
For example, if the amount is 100,00 and app_fee is 10.00, then the payer will receive a refund of 100.00, where 90.00 is the net refund from the payment account, and 10.00 is the app_fee refund. Note that this value must be less than the remaining balance of the app fee.