Hey creiht, yes the skill die is intended to be used for all skill checks and acts as a simplified way of measuring their competence (like the monsters skill die).
As the referee, you could make a ruling to decide where it may not be appropriate to use though (i.e. magic checks for example as any magic casting people are likely to have hero status and not a run of the mill NPC status)
Thanks for the question, hope the clarification is of use (and it's a subtle way of me getting some feedback on things which may be obvious to me I wrote it but not so obvious to someone who is reading the rules).