I'll guide you through the steps to accurately record your CIS deductions so your payment reflects as fully paid, fmaplastering.
In QuickBooks Solopreneur, it's necessary to enter the total amount charged to the contractor under the CIS labour standard (20%) line item. Adding separate line items for additional services or products could result in incorrect invoice calculations, potentially leading to a higher total invoice amount.

Once you correct the entries, the invoice should no longer show as partially paid.
To verify the accuracy of the calculations and ensure they align with the payment amount, you can review the details in the designated section on your invoice page. Please see attached screenshot:

This way, you can confidently manage your financials without discrepancies.
I'm attaching this article that can guide you in seamlessly handling your CIS: CIS guide in QuickBooks Online.
Reply to a comment if you need further assistance with CIS. I'm here to help you in any way I can.