I want to credit an sales invoice which includes CIS. When I try to do credit note it does not include the CIS, how do I credit this?

Hi there, MJ666.

Welcome to the QuickBooks Community. I'm here to help you apply the credit note to an invoice in QuickBooks Online.

When creating a credit note, you'll have an option to add the CIS item and add the final amount deducted from the percentage. You can check the screenshot below for your reference:

Once done, you can receive the payment by applying the credit note to the invoice.

Here's how:

1. On the left panel, click Sales.
2. Go to the Customers tab.
3. Click the customer.
4. Search for the invoice and click Receive payment.
5. Put a check mark on the invoice and credit note.
6. Enter necessary information.
7. Click Save and close.

Please be sure to let me know if you need further assistance with the process, and the Community is here to help.