Zakat(via payroll)

The Zakat amount will be deducted from the employee's salary. The employer will pay the Zakat office on behalf of the employee. This amount will reduce any PCB payable. 

For example, the employee has to pay PCB in the amount of RM150. After the deduction of Zakat(eg RM50), the PCB payable would be RM100.

Zakat(via TP1 form)

The Zakat amount is paid to the Zakat office by the employee themselves. That means it wouldn't be deducted from the employee's salary. After payment, the employee has to submit the TP1 Form to inform the employer of the amount to be deducted from the PCB. Like the Zakat(via payroll), this amount will also reduce any PCB payable.