I'd like to help you get this sorted out, MHC.
If you have recorded the payment using the Write Checks option, this will not affect the tax liability that shows due in the payroll center. However, this process clears out your payroll liabilities report.
You can either leave the alert or create a custom payment to remove the tax due. I've got this article for the instructions: Set up and pay scheduled or custom (unscheduled) liabilities.
Please let me know if there's anything else you need. I'll be around to help you some more. Thanks.