Refunds for pay-by-check orders are the responsibility of the farmer, and subject to the rules of your CSA. Please be sure to convey to your members what your refund policy is; this can be added as a note during the Order Confirmation process.
Refunds to members paying with credit cards are through the originating order. In the order you will see in the lower right corner a Refund button. Note that you can refund back to a member credit card (default) or to their cash account (to be used for future orders.) If you are issuing a refund and canceling the subscription, be sure the 'cancel refunded subscriptions' box is checked.