You are right. The black heavy black line is the nut before the first fret on the neck. Later as you learn chords further up the neck, you will see a number beside the fret closest to the nut. It represents the fret your starting from. ie, a 5 would mean that the 5th fret was the base fret at the top of the diagram.
I looked at the pages you were talking about. I think your talking about bar chords. You use your index finger to make an artificial nut further up the neck. The dots for the fingers or chords stays the same. ie, an E chord played down at the nut is the same shape as a barred G chord at the 3rd fret. It just goes up 3 tones from E to G. Hope that helps.
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