I have logged a cis suffered in payroll but it has not registered in the eps file to submit to hmrc. I am self employed and have cis taken from the contractor.

Hello, @Kevinkelsey71. 

I can show you how to enter CIS suffered to be ready for submission.

Here’s how to enter CIS suffered: 

1. Click on Employees on the left menu and select Enter CIS Suffered.
2. On the CIS deductions panel, enter the current CIS deductions for the year to date in the Amount deducted box, and Date for deduction calculation box. 
3. Select Save once you’re done. 

Check this article for more information: Record Deductions Suffered under CIS. 

I'm always here if you still have questions. Let me know by leaving a comment below. Have a wonderful day!