"My fiancee and I have decided to get married in the Philippines but we already applied for a fiancee visa. So how much paperwork is involved and are we starting over?"
If you filed for a fiancee visa and you got married, you're no longer eligible for a fiancee visa so that would require you to start over. As soon as they find out you're married, you would not be eligible for the fiancee visa and that would be denied. Fiance visas are for unmarried couples intending to marry, while spousal visas are for married couples.
If you have an active case with the USCIS, you're going to have to submit a letter and request that they cancel that. You don't want to have more than [one] active application in the system because it may appear like immigration fraud and that's the last thing you want with immigration.