Your confusion comes from the fact that the normal rules and the Pathfinder Society Organized Play rules treat XP differently. In normal gameplay, you gain variable XP based on how the threat compares to your level, how big your party is, etc. But in organized play, where everything (party size, average party level, and so on) can vary so much from playthrough to playthrough of a given scenario, their XP system is vastly simpler - one XP per scenario, with three XP needed to level up. That way it's much easier to track.
Where XP is a measure of the competence your character gains at doing their thing, prestige (a Society-only system) is a way of tracking your favor with your boss, the Pathfinder Society. You can then spend that favor how you see fit according to the PP guidelines, on equipment like wands or services like resurrection.
Hope that clears things up a bit!