Hello again, johnfilas.
I can help clarify why you’re unable to see the SEP IRA Employer in the Custom Payments screen.
This can happen when the account used to track the payroll item is not a Payroll liability. You’ll have to review the setup and update the information to resolve this issue.
After completing the process, you’ll see another window asking how you want QuickBooks to update the transactions. Make sure to read the options and select the correct one.
With these steps, you should now see the deduction item and will be able to create a liability check.
Keep me posted on how these troubleshooting steps work for you. I want to make sure everything is taken care of and you're all set with this concern.