Supplier Debit note and refunds

We have received a supplier credit note - debit note which i have entered on their account. They have issued us a payment against the credit note. How do I allocate the payment to the supplier debit note? At the moment i have posted the cheque to the bank, but their account is now showing in credit on their transaction list - and the debit notes to not appear?

Thank you

I assume you mean the Supplier Statement? If so, is the report set for Transactions, or only Unpaid Invoices? If for Transactions, are the beginning and end dates correct?