I need to pay one of our employee a referral fee, but on a separate payroll deposit and to ensure it takes deductions?

Hi there, 

Running a separate pay run for your employee's referral fee is simple to do in QuickBooks Online. I want to make sure you're setting this up properly so that deductions are calculated accordingly. 

I'd recommend running a bonus-only pay run. Using the "Bonus" pay type in QuickBooks Online means that deductions are still calculated. You can set this up in both Standard and Advanced Payroll.

To create a separate bonus cheque in Standard Payroll, follow the steps in this article: How to create a bonus pay cheque.

For information on how to set up a bonus pay-type in Advanced Payroll, refer to this article: QuickBooks Online Advanced Payroll - Pay & tax settings. To see how to run this in Advanced Payroll, check out this article: How to run payroll.

That's all there is to it. If you have any other questions, please feel free to reach out in the comments down below. I want to make sure I've fully answered your question. 

Cheers!