What should I do when the instructions say to allow my thoughts to go where they want, not to judge them, to stop focusing?

This is part of learning the method suggested by Petit BamBou. The idea is to note/observe your mental functioning throughout the meditation session, becoming conscious of what is going on inside you, even without instructions.     

Abandoning your focus means no longer restricting your attention to focus on the breath, the points at which the body is in contact with the underlying surface, or your thoughts. But allow your attention to go where it wants (sometimes you will discover it to be quite timid in this type of situation).