You can apply a credit back to the persons credit card by going into the Transaction Record and clicking either Refund or Partial Refund. You can only refund transactions that have already settled with the credit card company.
If you activated the packaged Workflow rule "Invert Refund", the Transaction "Amount" field will become a negative (ChargentSFA__Amount__c * -1 ) so as to total properly in the rollup summary fields "Transaction Total". Clicking Refund on the main Opportunity, Order or Case page, will attempt to refund ALL related transactions, which you probably did not intend.
For more information on refunds, please see our Documentation page.