That would be "you had" contracted to you'd. "You had better (do something)" is a way of saying you should or you must. The kind of phrase my mother might have told me "You'd better have cleaned your room by the time I come upstairs!" or "you'd better be awake and ready for school by 8am!" It has a softly threatening tone, implying that there is a negative consequence if you have not done what has been said. Such as in the lyrics you posted we could also say "you should run because WITCH will strike together if you don't" Hope that helps :)