Hiccup in the fanfiction typically trains by forming strong bonds with the dragons first. He shows them kindness and respect, and then gradually introduces training exercises that are fun and challenging for both him and the dragons.
Hiccup can be abandoned in fanfiction for a multitude of reasons. It could be that he's seen as a liability, or there could be a prophecy that leads others to believe he should be left alone. Sometimes, it's just a plot device to drive his character development and adventure.
Well, in these fanfics, Hiccup being a ninja usually means he has to master the art of moving silently and quickly. He might have secret missions or have to fight against powerful foes using his newfound ninja abilities. And it could add a whole new level of excitement to the How to Train Your Dragon universe.