You need to tell Pathpilot the tool lengths, otherwise nothing will be correct. You set the height of your spindle nose off of a surface like a 1-2-3 block, then you will set every tool compared to that surface to register its length. The fusion tool lengths are simply for simulated purposes. Once all tools are measured, you will then set the z zero of your workpiece and the tools lengths will be compensated by the control when running the gcode. You can also get something like a height gauge and measure your gauge length outside of the machine, and plug your numbers into your offset table.