In Rhino, both the object that you will be working on and the mesh that represents your tool should reside at 0,0,0. The tool mesh is only for visualization purposes. The important data is the tool number, the base number, and the accompanying measurements.
KUKA PRC is going to take the measurements of your tool (as entered by you manually) and the measurements of your base (again entered manually) and use them to offset the work by an appropriate amount when it writes the final code for the machine.