In the Stomp section choose the Line 6 Bender.
If you assign the onboard pedal to Tweak and set different pitches for heel & toe positions, you can change pitch with it as you play. For a whammy bar effect you could set heel to 0 and toe to whatever pitch you want to bend up to.
To get harmony, use a Dual Tone setup with the above on tone 1 and no Bender on tone 2.
I use it in the middle of Pink Floyd's 'Hey You' for a harmony riff that alternates between minor and major 3rds.