Secondary rays are all rays except primary. This may sound cheeky perhaps, don't mean to be cheeky, but as soon as a primary ray hits a volume/surface and bounces it undergoes a change and becomes a secondary ray.
At least, that's what I understood of the concept. Basically primary means visible to camera and secondary visible to other rays.
This was why I thought that disabling secondary in the cloud turns the clouds invisible, because it would make the cloud invisible to the refracted rays from the water plane/object.