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What's added in the Classes tab is the Class Level - then, the class level bootstraps the class helper. Since the Class Helper is unique, only one copy for each class the character has ever gets onto the character.
The editor manual is what you should read first (from the help menu within the editor) - that deals with the d20 files specifically. The Authoriing Kit wiki is mostly about building a game system from scratch. Looking at existing things, and seeing how they go about what they're trying to do is my recommendation for a second step. For example, if you want a feat that adds a bonus to a specific skill or two, that sounds close to the various skill A + 2/skill B +2 feats, like stealthy.
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