Could you clarify how/where you are entering the X,Y,Z coordinates? This example is taking its direction from the 'Waypoints' block as described in Task 2 of the example documentation (Configure Waypoint Follower and Landing Logic in Path Planning Subsystem). The VSS_COMMAND (Flight Commands) options, which includes the joystick input you mentioned, are not utilized directly. I did try changing the height from 1 to 3 meters (i.e. from -1 to -3 since Z points downwards) in the 'Waypoints' block and got a Stop Simulation error flag after 5 seconds of flight. Is this what you were experiencing?
If you have not seen the following quadcopter example I recommend taking a look.
Besides the joystick option (VSS_COMMAND=1), you can also modify the trajectory using previously saved MATLAB data (VSS_COMMAND=2) or spreadsheet data (VSS_COMMAND=3). Sample data files are in the 'mainModels' subdirectory.
