You should be able to leave the MIDI Output in Quick Controls setup Not Connected.
Did you use the “Learn” mode in Quick Controls setup (Device Setup)?
Once you have done that you can enable the “L” learn mode in the track’s inspector Quick Control area. Enable “L”, select the slot you want, and then click your mouse on the wah pedal and rock it (the virtual Amp Rack pedal - don’t try to use your mouse to operate your foot pedal 
). Your foot pedal should then be operating the Amp Rack wah pedal.
I’m thinking maybe you didn’t get your foot controller “learned” properly in Device Setup → Quick Controls?