If you're using E Phrygian, then yeah you're using all the same notes as C Major
If you meant the relative Phrygian Mode in E natural minor (B Phrygian) then you're using 6 or the 7 notes in C major, the only difference is your F note in the scale is sharpened to an F# (this is not in the C Major scale) - B Phrygian would be instead using all the notes of the G major scale.
Hope this helps and hope you're well