In the harmonic mode, the EBow adds harmonics to every note you play up to the higher registers, where it increases the EBow sustain range.
In the standard mode, harmonics can be achieved by sustaining notes fingered near the nut, the first 5 frets or so, on the E, A, D and G strings. As the EBow is moved away from the pickup and toward the bridge, the string tends to vibrate with more of its upper harmonics. Bends and vibrato help get the harmonics started and add color to the sound.
To avoid harmonics, don't finger notes near the nut of the guitar. Or, muffle the string slightly with your right palm, behind the EBow, near the bridge.