It sounds like you have the modifier on the sphere and are trying to point it at the particles, or something to that effect. The Krakatoa SkinWrap should be placed on the PRT Loader, and the pick button should be used to select the Sphere object.
Just to clarify, the Krakatoa SkinWrap can be used to animate a particle cloud, based on the deformation of a geometry object. It does not support the inverse operation.
I’ll ask Bobo to make a short tutorial for the SkinWrap in order to clear up any outstanding issues.