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Hello there, ameyerovich1.
As my colleague shared above, if your employees use direct deposit, there's no check number to be arranged as there's check deposited.
If you use checks to pay your employees, you can prevent the system to assigned a check number automatically by deselecting the Print Later field on the QuickBooks Desktop.
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For additional reference, you can check this article to learn more about Direct Deposit: Online Payroll – Direct Deposit FAQ.
I'll be around to help you out. Keep safe!