Thank you people.
It appears that different people do different things.
If I have read the responses correctly, some people do add the Skill Category Bonus to the written value for each skill, while others do not.
Some people have it that the Bonus effectively does not impact the success of an Experience Check Roll, while others have it so that the Bonus does make a difference.
So I guess the real answer is there isn't an official correct way. Instead use whichever the GM and players are happy with.