How do i set the 20% CIS deduction on my invoice so the invoice matches the payment into my account

I'll guide you on how to deduct CIS on your invoice, userdarren-snell1.

First, you'll want to enable CIS in your settings.

1. Click the Gear icon > Company Settings (or Account and Settings depending on what you see).
2. Click Advanced.
3. Select Construction Industry Scheme (CIS).
4. Enter your info and click Save.

Second, go to your customer's profile and check the Is CIS Contractor checkbox.

Third, when you create an invoice for the customer, enter the amount in the Less CIS field.

You can also check about CIS in QuickBooks Online for your additional reference.

If you have other questions, you can always go back to this thread.