If you need to make a payment from your Agency account, but the payment details have not come through the payroll to agency process, you can create a Manual Agency Check.
From the Payroll > Agency > Create Payments screen, click the Manual Check button:
After clicking the Manual Check button, the following window opens. Complete the fields and click the Create Manual Agency Check button.
Once the payment is created, process it as you would normally process an Agency payment, including creating a Purchase Order.
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