E-phrygian,
I think I've realized part of your confusion. When playin in a mode (E Phrygian, for instance), you do not change your scale you're using. You will always be in a C-Major scale (like B3 said).
If your song changes to F, you are still in the E-Phrygian mode/C Major scale. You may change some of your "landing" notes in your lead to compensate for your chord changes, but it does not actually change the scale or mode you are using.
By your example, if you reference your notes from the starting point of F, still using the C Major scale (as I believe you were), you have effectively changed your mode to F Lydian, because you are now playing a C Major scale over F, not E. You will continue to reference E to stay "Phrygian."
Chords are generally irrelevant to modes, also. Certain modes sound better over certain chord progressions (which is what I posted above--some modes are minor-flavored, some are major flavored, one is diminished), but there are not really "phrygian" chords, per se. The way you have it written, you are trying to make chords out of the E Phrygian scale. Remember that these notes are just C Major--you've only changed which note is your root (or tonic). So, if you try to construct chords with these notes, you will get the same chords you would get out of dissecting a C major scale, only the order you put them in your prog. may be different. The basic chords you can make out of this scale are (without embellishments like your seventh's, etc.) Em, F, G, Am, Bdim, C, Dm.
Regardless of what chord, though, if you're in E-phrygian, you stay in E-phrygian(C-major scale). I guess if you want to write something "phrygian-sounding" you can basically pick any of these chords from above and make up a prog. It's going to sound dark, it's going to sound a little flamenco. Try (soundng this out in my head) Em - F - Em - C - Bdim - Am (use Bdim as a pasing chord).
I know I can't show you the feel of a prog. on a post, but play around with stuff like that if you're looking for a phrygian feel.
BTW, are you writing a heavy metal song? Just kidding. But that's where this mode is predominantly used--80's speed metal. I find it hard to adapt to much else. It always has that heavy sound.
Hope that clears it up a little.