Here's my 2 cents.

James - you said you mapped out E phrygian, and did it correctly. You said that phrygian is the 3rd note of a scale, but it is the 3rd note of the major (ionian) scale, not just any scale. Because A minor is derived from C major, E phrygian is the 3rd note of C major. Relative to A minor, E phrygian is it's 5th mode. All modes are relative to one another provided they're in the same key.

As a side note, let me add the following. It gives you the modes relative to the mode you are playing in. I hope it's not too confusing.


Ionian

I - ionian
ii - dorian
iii - phrygian
IV - lydian
V - mixolydian
vi - aeolian
vii° - locrian


Dorian

i - dorian
ii - phrygian
III - lydian
IV - mixolydian
v - aeolian
vi° - locrian
VII - ionian


Phrygian

i - phrygian
II - lydian
III - mixolydian
iv - aeolian
v° - locrian
VI - ionian
vii - dorian


Lydian

I - lydian
II - mixolydian
iii - aeolian
iv° - locrian
V - ionian
vi - dorian
vii - phrygian


Mixolydian

I - mixolydian
ii - aeolian
iii° - locrian
IV - ionian
v - dorian
vi - phrygian
VII - lydian


Aeolian

i - aeolian
ii° - locrian
III - ionian
iv - dorian
v - phrygian
VI - lydian
VII - mixolydian


Locrian

i° - locrian
II - ionian
iii - dorian
iv - phrygian
V - lydian
VI - mixolydian
vii - aeolian