Thanks for adding some details of your concern, info1403.
Unfortunately, we're unable to match the two payments to a single transaction since their amounts aren't the same. Please take note that we can only match transactions with the same amounts in QuickBooks Online.
To ensure that your payroll records are accurate, you'll have to exclude those two downloaded transactions on the Banking page. Once done, you'll have to manually clear them in the register so you can easily reconcile the transactions. I'll show you how:
I also encourage reading these articles to help manage your downloaded bank transactions in QuickBooks Online:
I'm just a few clicks away if you have any other concerns or questions about bank transactions and reconciliation. I'll always have your back.