The Cintimani-Bearer has five quests in a single quest set, not five quest sets. For each story, you'll use that quest set, rearranging its quests in the order appropriate for the type of Arc you want that story to be
As for writing your own quests and stories: Think of the premade character archetypes and storylines as a campaign module. Once you have a grasp of the pattern from the samples, you can write your own material for a more personalized campaign (and the descriptions of how quests and arcs work are there to help you with that!)
However! From my own experience playing the game, there's still plenty of surprise and improvisation. You can see that the premade quests and stories give you a lot of questions, but don't give you the answers. Finding the answers is where the real game is.