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Is it a bad idea to insert the cards for class decks I'm not using characters from in the base set?
I'm not quite sure I understand the question. Class Decks are these things:
Pathfinder Adventure Card Game: Class Deck – Monk
Pathfinder Adventure Card Game: Class Deck – Fighter
I would only add them if you were playing a character from them and then only if you looked at the cards in the adventure path and thought your character would need the cards from the class deck.
If by "class deck" you meant the suggested character decks at the back of the rulebook, then any card not in you actively played character's deck should be in the box. (At least until adventure 3 when you are instructed to start removing cards from the game.)
I hope that helps.