When creating an invoice with CIS applied you may want to apply the CIS deduction to the labour only, and not the materials. There is two ways of dealing with this in KashFlow.
Methods
Set up Exclusions (Recommended)
To set up exclusions, which tell KashFlow not to apply CIS on certain Sales Types go to Settings > CIS Options > Tick Exclusions. You can then list the codes used for materials so that when the CIS is calculated any invoice lines assigned to these codes are ignored. An “Add Deduction for CIS” button will appear once you have added all line items to the invoice.
Add Labour first
Alternatively you can enter the line items for labour first, save the invoice and click on the Apply CIS discount button which will appear on screen. This will apply the CIS deduction on the labour only. Afterwords, you can enter the rest of the line items not subject to CIS.