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I appreciate the details you've shared, @Warpa. I'll route you to the best department that can help you further with manually entering cis payments.
Before anything else, have you turned on CIS in QuickBooks Online? This feature will help you in calculating and deducting payments, then submitting them to HMRC.
Since it involves personal information, I recommend contacting our Support Team. From there, they can guide you in recording them properly so you can file your tax returns correctly.
Here's how:

See this article for the support hours: QuickBooks Online Support. It includes the contact number you can use to call us directly.
For more information about managing CIS transactions, refer to these resources:
Let me know if you need further assistance while working in QuickBooks. I'll be right here to help. Take care.