Regarding suggested values, yes that is after chargen and points have been spent (AFAIK), but there's no reason you can't just call it 13 to start off with, and have it rise over time with failure as @Oracle suggests above.
Regards what ability you use that's entirely up to you and character dependent. If you take your example of Compulsive, the GM would try to roll equal or under to that flaws value and you would roll appropriate to overcome it, e.g. if you're trying to resist doing something you could use your discipline as a 'Warrior Prist of ....' - anything you can up with that's narratively appropriate.
In regards to overcoming the Corruption flaw, the character could perhaps use his magic ability - masters of the art are more likely to understand the risks and mitigate them perhaps? Or some other ability that suggests mental fortitude.