Ok here's a follow up question on modes. I've been messing around in the key of A minor, and I was trying to find other positions on the fretboard to play the A minor scale (besides the one based off the 5th fret, 6th string), so I decided to start in the open position (so the root is E). Well I mapped out the scale, put the half steps between BC and EF and boom I got the A minor scale. So I thought. While at first it sounded similiar, I realized that I had created a mode of A minor. It sounded very middle-eastern so I thought, this is phrygian, and when I consulted my chart which said:
Phrygian- m2,M2,M2,M2,m2,M2,M2, and lo and behold, the half steps coincided with the chart. But the phrygian mode is based on the 3rd note of a scale, isn't it? And E isn't the 3rd of A Minor, C is. So what did I do?

Sorry for the confusion, I realize this question is really messed up.