Pitch axis theory is cycling through different modes with a constant bass note. It's using each of the 7 diatonic modes with the same root. Just like the circle of fifths (a progression through multiple scales), there is a certain order to the progression of modes that sounds best. Lydian, Ionian, Mixolydian, Dorian, Aeolian, Phrygian, Locrian.

Lydian - 1, 2, 3, #4, 5, 6, 7
Ionian - 1, 2, 3, 4, 5, 6, 7
Mixolydian - 1, 2, 3, 4, 5, 6, b7
Dorian - 1, 2, b3, 4, 5, 6, b7
Aeolian - 1, 2, b3, 4, 5, b6, b7
Phrygian - 1, b2, b3, 4, 5, b6, b7
Locrian - 1, b2, b3, 4, b5, b6, b7

Example : C Lydian (C, D, E, F#, G, A, B) to C Ionian (F# -> F) to C Mixolydian (B -> Bb) to C Dorian (E -> Eb) to C Aeolian (A -> Ab) to C Phrygian (D -> Db) to C Locrian (G -> Gb)

Now, each step in the cycle changes only one note, but from the first mode to the last, there is a huge sound difference (C, D, E, F#, G, A, B -> C, Db, Eb, F, Gb, Ab, Bb). Satriani really emphasizes the notes that change each step. He really hammers the E going to the Eb from Mixolydian to Dorian. For a really good example, pick up "Engines of Creation" by Satriani and check out some of the latter tracks, such as 8 and 9 if my memory serves me correctly (don't have the cd here with me and I'm too lazy to go get it out of my car right now).

Feedback: Clarified? More confused? I hope that helped...