Last year I changed my old green passport into married name even it's not yet expired and the DFA office in Cagayan de Oro asked me about the CFO certificate so what I did was I went to Cebu and had the seminar there for half day then went back straight to the DFA Office in Cagayan de Oro the next day morning.
She will need to attend the seminar first and then get the CFO certificate before she can change her passport into married name and then when you apply for her visa and her visa will be approve then that's the time she will need to go back either Manila or Cebu for the stamp/sticker.
About using the agency for changing the passport I'm not really sure because I think they will need the personal appearance of the applicant.