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 asBusinessIncome. 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: