After you've become comfortable with the first scale position, it is important to learn a different place to play the same scale on the neck. This second diagram illustrates the harmonic minor scale, with the root on the fifth (or third) string. So, if we wanted to play an A harmonic minor scale using this position, we'd find the note A on the fifth string (12th fret), and line that note up with the root of this scale position (highlighted in red). We could then start playing the scale on the 12th fret of the 6th string. This might take a bit of practice to find quickly, since our starting note in this position isn't the root of the scale.
You'll want to start this scale with your 2nd finger. When playing the notes on the fifth string, start with your first finger, then slide your first finger up a fret to play the second note on the string as well. Stay in this position for the remainder of the scale.