I think you have to use the interval training settings, configure it to use "distance mode", and enter the route sections there. If you'd include heart rate in a GPX file, Run.GPS would simply ignore it when reading the file.
I also work as a coach so, need to set tasks for my sportsmen. And it's will be very nice to have possibility to set pace and may be heart rate interval for parts of the route in route planner. And then use it like virtual lead track. Maybe somebody knows some external application which can make such GPX files?