We got married in Cebu earlier this year, although in a church rather then civil. If you want to talk to my wife about it I can give you her number in Cebu, she's in Cebu for a week or so until she flies over to Muscat and would happy to explain some of the processes.
I have a friend who is a British-Australian expat living in Cebu and running a specialist business with his Filipina wife Elsa. The website is
www.cebuexpatservices.com and they do a lot of wedding planning, and knows the processes back to front and can do the legwork if you'd prefer. They are very trustworthy, and have straight up clear prices, and have agreements with many local hotels and facilities. Although we didn't use them for wedding planning, they did provide a band for our wedding who were absolutely fantastic. Just tell him that Ricky and Marvie sent you.
One thing that we did do was negotiate with the venue a corkage fee and bought a lot of alcohol from Makro and an outside caterer. The big reason I did this was because I knew that some of my Filipino relatives would struggle to afford the hotel alcohol prices, and I really wanted people just to enjoy the wedding without worrying how much money they are spending.