Hello Jwhits,
Thank for the additional information.
If the second payment is showing in the For Review tab, you can add them in QuickBooks Online and allocate them to the Accounts Payable account in the Category field, and make sure to select a specific supplier before adding the transaction. With (Out of Scope of GST) tax code. That way the overpayment will show as Credits on the specific supplier you made the payment to and can apply to your future bills.
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