Hi info302,
To use CIS in QuickBooks Online you'll first need to turn this on by going to the Gear icon > Accounts and settings > Advanced > Enable CIS.
You can then setup your contractors as customers in QuickBooks by selecting the 'Is CIS Contractor' checkbox on the Customer information tab when creating or editing a customer.
QuickBooks automatically generates the chart of accounts and reports you need to track CIS when you turn this on - you can see the accounts by going to Accounting > Chart of Accounts and entering 'CIS' in the search-bar.
To create the invoice, go to the + icon > invoice, enter the customer (contractor) on the drop-down, and select the relevant CIS 20% account under product/service. Then enter the total amount on the invoice line and QuickBooks will calculate the 20% deduction, shown below the subtotal as 'Less CIS'.
You can see more on CIS in QuickBooks here :)
Thanks!
