For excess, there is nothing you can do in the system, as the excess has been paid out to the CPF Board.
You can only claim the refund from the CPF board; the CPF board will return it to both the employee and the employer. During the year-end Income tax processing, you need to enter the CPF refund information in IR8S Section C.
If you choose not to get the refund for your employee, then your employee will be taxable for the employer's excess CPF contribution. In this case, you do not need to enter the refund information in the IR8S Section C.