Hi, both ways are correct.
The harmonic @ the 5th fret on the E string produces an E note (ie: an interval of a fifth higher than the actual note A).
The harmonic @ the 7th fret on the A string also produces an E note (ie: the same note as the fretted note). So, when you play this, and the low open E string, you can tune with them.
I tend to tune using the first method, and then do a quick run down the strings using the second method.
Hope this helps...
