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Check what feats the characters have -- for example if the wizard in question has the great fortitude feat he would get a misc +2 modifier to his fortitude save.
As to the skills you have it correct.
Anything that provides enhancement, trait, racial, etc bonuses to skills usually get lumped into that misc column. Just keep in mind that bonuses of the same type don't stack and that you only take the strongest. So, if you get a +2 trait bonus and a +4 trait bonus to a single skill only the +4 applies and the +2 just sits there all alone not being used, poor guy. :P That said, untyped bonuses do stack. So, if that +2 were simply a bonus rather than a trait bonus the character in question would gain +6 to that skill.
you give a +3 to any skill that you have added a rank to and that is also a class skill
Not quite. You get a +3 bonus to the skill roll, not to the actual skill rank itself. In most cases that distinction is moot, though.
Anything that provides enhancement, trait, racial, etc bonuses to skills usually get lumped into that misc column. Just keep in mind that bonuses of the same type don't stack and that you only take the strongest. So, if you get a +2 trait bonus and a +4 trait bonus to a single skill only the +4 applies and the +2 just sits there all alone not being used, poor guy. :P That said, untyped bonuses do stack. So, if that +2 were simply a bonus rather than a trait bonus the character in question would gain +6 to that skill.
The Beginner Box doesn't have types of bonuses, so you don't have to worry about whether or not certain bonuses can be used with other bonuses.