If you are using your CPF savings to pay for the fees of more than one student under the CPF Education Loan Scheme, the deduction will take place based on the payment date to the institution. For example, if the payment date for Institution A is 1 Feb and for Institution B is 3 Feb, the savings will be used to pay Institution A first before paying Institution B.
If there are not enough savings in the CPF account, the student will have to pay for any shortfalls in cash, to the approved educational institution.