Right, it appears that both items should be used together. You raise the truck with the spacers, then you "fool' the sensors to think that you are still at stock ride height.
That way your air-bag/shock remain the same length that they were originally. And just as important the pressure in the air bag isn't increased to raise the truck.
I think what you were experiencing was the increased air pressure in the air bags as well as the upper limit of the shock's travel.
I'm glad to hear that you seem to have it sorted, please let us know how it works out.