How do I match payments to invoices when 20% CIS payments have been deducted.

I can help you with matching payments to your invoices with CIS transactions, @chris-sleafordhv.

You can go to the Transactions tab and then select subcontractor or contractor to let us know it's a CIS transaction to match this payment. 

Follow the steps below: 

1. If you're in a Business view, go to your Transactions menu. If you're in an Accountant view, go to the Banking menu and then Banking. 
2. Proceed to your For Review tab and click the transaction to review the details.
3. Choose a transaction type.
4. Select a subcontractor or contractor from the dropdown to let us know it's a CIS transaction.
5. Click Match or Find Match to calculate and apply the CIS to this transaction for you.

You can check this article for more information about matching or adding CIS transactions: How to create CIS transactions in QuickBooks Online.

To make sure that your accounts always match your bank and credit card statements, here's how to reconcile an account in QuickBooks Online.

Let me know in the Reply section if you need more help in matching payments to your invoices. I'm always here to help. Have a wonderful day!