How do I deduct CIS from an invoice so it it no longer shows as an outstanding payment?

Hello there, Mellymint. 

Once the customer is already set up for CIS Contractor, the CIS Labour Standard 20% line item will populate when creating an invoice. If the customer is already entered an the CIS line item didn't show, let's make sure that the Is CIS contractor is checked on their profile.

Let me show you how:

1. Go to the Sales menu and click Customers. 
2. Search and select on the customer's name. 
3. At the upper-right, click Edit. 
4. Verify if the Is CIS contractor is checked under the Display name as field. 
5. Click Save.

Then, let's create an Invoice and the CIS item will auto-fill on the first line. Enter the product sold on the second line with the VAT code. Once done, at the bottom part of the invoice, the CIS amount will show in the Less CIS box. 

You can pull the CIS reports to track your CIS withheld. Go to the Reports menu and search and select CIS Suffered Summary.

Let me know if you need more help!