How to post a payment when CIS period is marked as filed?

Hello Johall-Business, 

Welcome to the Community page, 

To account for the payment you make to HMRC following a CIS submission:

1. Go to create an expense.
2. If you have created a supplier for HMRC, then please enter the name in the supplier field.
3. Select the bank account from which you have paid HMRC and select the date the payment was made on.
4. In the table section, under the Account column select the CIS Payments to HMRC account.
5. Enter the amount you have paid HMRC.
6. Select Save and Close