So anytime you are doing something related to that role you would add +X.
For sneaky it might be picking locks, sneaking through the shadows, or other items your abilities let you do, but without using the automatic success of a slot.
For mystical this might be reading runes, or activating and uncontrollable magic object.
For Holy this might be sensing and evil presence or preforming a religious ritual.
Essentially the answer is "when it makes sense" but hopefully the explanation above is a bit more clear.
Also if you put both points in Sneaky you would choose both Hide and another ability. Every point in a role gives you an ability.