Add these to your template:

{TotalCISDeduction} - this is the total to be deducted from the tax due on the invoice

{TotalBalanceAfterCISDeduction} - this is the total of the invoice when the remaining tax is added to the net value.

Resulting in:

Import the CIS sales account code from the system that you are using.

Import the CIS sales account code from FreeAgent and select it on the invoice using the dropdown:

If this field is not visible, make sure you are connected to FreeAgent and the field is set to visible in the edit page's settings.

Add in a sales account code that includes 'CIS' in the name and description. Zigaflow recognises this and applies the calculations.

Select the CIS account code for the line item: