The following image shows the Flight Plan Screen (without fixed-wing tuning mission loaded):
The main window shows a satellite map of the mission area. The yellow lines represent the desired path of the vehicle, while the white circles represent the area for the turning arc (turning radius). The green markers represent the actual waypoint targets for the mission.
The bottom window is a chart representing all of the parameters for the mission. In this window, you can add events (such as Do Jump, which sends the vehicle back to a specific waypoint). If your camera is attached to Pixhawk, you can tell the camera to take an image/start recording. Flight modes can be set to change as well (such as "Land"). Any command Pixhawk is capable of executing can be triggered using this interface.
The window on the far right allows you to save missions for later use (to your computer), load previous missions, change the type of satellite map. Different maps can prove to be more/less...