Thanks for getting back to us in Community, @parkerupllc. I'm here to lend a hand so you’ll be able to turn off invoice direct deposit payments in QuickBooks Online.

You have the option to temporarily turn off direct deposit for an employee.

Here’s how:

1. Go to Payroll, then select Employees.
2. Select Run Payroll.
3. Under the Pay Method column, select Paper check.
4. Preview and submit the rest of your payroll as you normally would.

 
However, if you’ll want to make a permanent change to your employee’s pay method, you can change it in your employee’s profile settings.

Here’s how:

1. Go to Payroll, then select Employees.
2. Click the Employee's name.
3. Go to the Pay tab.
4. Under the no. 7 option, click the drop-down arrow and select Paper check.
   
   

 
With regards to the 2.9% fee charge. I would advise to reach out to our QuickBooks Online Support and have them check your account to see what’s really causing this issue.

Also, you can check this link for further guidance about this matter.

Additionally, you might want to print or reprint paychecks in QuickBooks Online (QBO), here's an article for detailed steps: Printing Checks and Pay Stubs.

Please let me know if you need clarification about managing your transactions in QBO, or there's anything else I can do for you. I'll be standing by for your response. Have a great day and stay safe.