There are 2 reasons why the CIS deduction Apply Charges button doesn’t appear on invoices.
Not enabled for customers
In Settings > CIS Options >Rate depends on customer/supplier is enabled then this could be that you haven’t enabled the CIS option for a customer.
This is enabled by going to Customers> Selecting a Customer> CIS & Other Info > Tick Apply CIS charges to invoices.
Now, when you create invoices for this customer you’ll see a button appear saying “Add Deduction for CIS”. You should only click this button once you have added all other lines to the invoice to which the tax applies.
Exclusions have been set up
You may have added a code to your CIS exclusion list, meaning no CIS button will appear for you to apply the deduction on line items with that code. You can view and edit the exclusion list in Settings > CIS Options.
If you’re still having trouble with this, let us know on firstname.lastname@example.org.