Welcome to the Community, @russ-cartmell-sk.
Currently, QuickBooks Self-Employed (QBSE) doesn't support and track CIS payments. Since these payments are happening outside the system, it'll not auto-calculate the deduction for CIS if you enter them after the taxed amount.
The system will only include the amount on the tax calculations are if you enter the full payment manually and tag or categorise them as Business Income. The system will then automatically account /include that income when calculating your income tax.
I'm also adding these articles that tackles filing CIS for future reference:
Please leave a comment below if you have any additional questions or concerns. I'm always here to help. Have a great day!
