Depending on how the second payment needs to be captured you could enter a "Supplier Credit" to capture the credit. When you have an invoice/bill from the supplier you can then apply the credit to it.
(Left hand side menu) +New - Suppliers - Supplier Credit
or if you are in Suppliers section
New Transaction - Supplier Credit
If you have a transaction showing up in your bank account for the second payment you'll want to record it as an additional payment through your bank (so that you can reconcile that bank account accurately). Make sure you add notes in the memo/description section that this is a duplicate payment which results in a credit on account. You'll need to apply the credit to a future invoice/bill so they clear.
