As what Sir Arthur have said, your wife needs to attend first the CFO seminar before she can use her married name. That is one of the requirements for the passport renewal.
She can choose where it will be convenient for her to attend the seminar- Manila or Cebu. I attended the CFO seminar (PRISM) in Manila last tues (2-16) and it just took less than 2 hours for the seminar and an hour to wait for the certificate at the CFO office. I will just have to come back for the CFO sticker when I have the visa.