When creating normal CIS Sales, there will be a balance which will need to be submitted to HMRC. The Clear Books accounts module does not allow you to submit these but you will need to use the Payroll module to do this instead. Please look at the guide below to see how this is done. You may also find this link helpful from the HMRC website HMRC Guidance
Ensure that your CIS sales invoices have their payment allocated to them. The CIS deduction will not occur in the File EPS in the Payroll module until this has happened.
Navigate to the Payroll module by clicking on the link along the top navigation bar.
Go to Employer > RTI > File EPS. This will take you to the RTI EPS form which needs to be submitted to HMRC.
Check the figure under the YTD CIS deductions from payments that they match the amount in your sales CIS.
Click on the Send to HMRC button.