I had to make a payment that I missed to SC Department of Revenue. How do I record payment on quickbooks?

Let's record the payment you've made manually, @cbuesing.

You can record the tax payment through Enter Prior Tax History. It will be a non-posting transaction and will not affect the bank register. 

Check the steps below:

1. Go to the Taxes page and choose the Payroll Taxes tab, then select Pay Taxes.
2. Select the Tax Type Name.
3. From the left menu, select Taxes & Forms, then choose Enter Prior Tax History, then select Add Payment.
4. Using the information provided on the Payment Due Details, enter the appropriate information.
5. Select OK.

Check this article for more information: Recording prior tax payments. Also, here's a guide that can walk you through on how to delete a tax payment. 

Please let me know if you have follow-up questions in recoding this transaction. I'm just around to help. Take care always.