How does the company produce a payslip that has deemed tax/NIC deducted when the actual salary paid to the employee is less? Should the entry on the payslip be actual salary or deemed emoluments with deemed tax/NIC deductions?

Payslips should only reflect actual salary and the tax/NICs on actual salary. The only employee documents where IR35 deemed payments and tax/NICs on them should be reflected are the P45 or the end of year P60.