Robotic loader motion planning

I'm rebuilding a robotic loader. I have a GUI built with GladeVCP hooked to a python state machine. (I am not going to run this robot with Axis or any other machine-tool-oriented user interface).

The state machine already has an interpreter that spits out waypoints, which depend on the state machine's internal variables. What's the best way to connect this to the linuxcnc motion planner?

I forgot to mention the state machine also has a "manual jog" mode, which I can use to move the machine if, for instance, I manage to crash one pallet into another.