I've been doing some work for a company who have been paying my CIS for me. I invoice them the full amount then they pay me minus the CIS part. Need to record this how?

Hello, kezwba. 

Thank you for the detailed information. To record the CIS Deduction, you can create a service item to offset the remaining amount they owe you. You'll have to re-open the invoice and modify it. But first, create a service item. Here's how: 

1. Click the Sales, then choose Products and Services. 
2. Tap New, and pick Service. 
3. Enter the information, and under the Sales price/rate enter the negative (-) sign and the amount. 
4. Press Save and close. 

Then let's open the invoice you've created and add the service item you created. 

1. Open the invoice to edit it.
2. Add the service item to the invoice. 
3. Tap Save & Close.

Another way is to Set up a clearing account and create a Journal entry this will help you offset the remaining balance, but I suggest contacting an accountant before doing so. They can verify what's the proper account to use. If you don't have an accountant, you can find one through this link: Find an accountant. I've added an article about how to set up a clearing account in QBO. Though this article is US region, but this also applies to the UK version: Set up a clearing account.

Also, to further guide you in managing CIS transactions in QBO, you can refer to these articles:

• Already using CIS in QuickBooks? 
• How to submit a CIS return in QuickBooks Online

Please don't hesitate to comment below if you have other concerns about the CIS scheme in QBO. I'll gladly help.