Hello Laura-accounts, 

Welcome to the Community page, 

So you need to make sure that VAT is turned on and CIS is turned on in the main cogwheel settings account and settings section and that you have also enabled the codes in the taxes section>edit vat>edit rates section as well. 

So on the invoice you can select the tax rate that says 20.0% RC CIS Domestic Reverse Charge for Building and Construction Services Standard.