Assuming you also use Cash Management and Account Receivable:  You don't void the payment because the check was cashed and will need to be cleared in Cash Management.  The refund will be deposited and recorded through Accounts Receivable as a Miscellaneous GL receipt.  The GL account you use to record the deposit will be the same GL account you used when you paid the invoice.  Lastly, if this is a vendor that receives a 1099-Misc, you will need to edit the vendors current year 1099 amount paid. 

Sage Knowledgebase article 18807 "How do I enter a refund from a vendor in Accounts Payable?" explains how to process a vendor refund using Accounts Payable and Cash Management.