Hello Michael, thanks for coming to the Community your query To account for the payment you make to HMRC following a CIS submission you can do the following
In QuickBooks, select + New and create an expense.
If you have created a supplier for HMRC, enter the name in the supplier field.
Select the bank account from which you have paid HMRC and select the date the payment was made on.
In the table section, under the Account column select the CIS Payments to HMRC account.