What is the best way to invoice as a CIS sub contactor? If I invoice without including it on the invoice then they take the 20% off, surely it will appear I am missing 20% of my payment?

Good day, darrencryer-gmai.

I understand that you need to create an invoice as a CIS sub contactor. We're unable to track CIS transactions in QuickBooks Self-Employed. You'll want to switch to QuickBooks Online instead. 

Please check this article for more details: CIS in QuickBooks Online.

Also, I suggest reaching out to our Customer Support Team so they can further assist you and see if there's a workaround in QuickBooks Self-Employed.

Post again here if you have more questions. Stay safe!