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Thanks for your post. You will need to process the electronic payment for that pay transaction only in Prepare electronic payments. You don't need to upload the ABA file to your bank, but, processing the electronic payment will move the amount from the electronic clearing account to the bank account.
When a pay run is recorded the gross amount is allocated to the Wages & Salaries expense account. If you record a Spend money transaction allocating the net amount to the Wages & Salaries expense account you inflate the wages expense resulting in incorrect financial reports. As such, you will need to unmatch and delete the Spend money transaction.
Please let me know if you need further help.
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