Welcome to the Community. I'm here to assist you with any question you may have concerning QuickBooks Self-Employed.
Right now, the Self-Employed version of QuickBooks 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 time QuickBooks will only include the amount on the tax calculations are if you enter the full payment manually and tag them as Business Income. The system will then automatically account /include that income when calculating your income tax.
In case you need additional insights about using QuickBooks Self-Employed, you can visit the help articles on this link:
Please remember I'm always available anytime you need assistance with your QuickBooks Product needs. You can reach out to me by posting a response.