The Primary and Secondary knobs control the level of the two octave shifts. The Pitch control determines whether the shift is up or down (and by how much).
This is how the Rainbow Machine behaves as well.
From the EQD website:
"The Secondary (7) control adds an octave of the Primary harmony. When the Pitch control is above noon, Secondary adds an octave above the harmony. When the Pitch control is below noon, the Secondary control will add one octave below the harmony. With the Pitch set to noon, the Secondary control adds an additional chorus voice for modulated, triple-tracked tones."
However this description is slightly inaccurate, because the second harmony isn't necessarily an octave up or down... It's double the interval set by the Pitch control. For example, if the Pitch control is set to one semitone up then the Primary voice is one semitone up and the Secondary voice is two semitones up.