Bjørnssp wrote:But I am a bit confused as to how these two pedal work,
If you got the Swell Pedal to work by using Right Click and then moving the Pedal, so your Swell Pedal now controls the image of the Swell Pedal on the Screen, then you are on the right track. The function of this one is to control the Swell Shutters (effectively, the Volume) of just one division (Keyboard) of the Organ. Probably the upper Manual, if I recall correctly. This is independent of which Channel is used for the actual Midi message.
The other expression Pedal on the Organ is called "Crescendo". You can activate it in exactly the same way, either instead of your Swell Pedal function (which can always be re-assigned later) or using a different Expression Pedal in case you have two of them hooked up. Again, you don't need to worry about the actual Midi message or Midi channel used (as long as the two pedals, if you do use two, are not both sending the identical message).
The "Crescendo" function affects the entire Organ (all divisions), by adding Stops progressively as you depress the Pedal further. (You will hear them, but not see them on the display.) And progressively removing Stops as you raise the Pedal back up... leaving only your original Registration when you are done (those Stops already activated do not get removed).
Hoping this is helpful, and Enjoy your new Organ!