Planning missions is straightforward: Switch to the mission view, click on the plus icon in the top left and click into the screen. The waypoint list on the right allows to modify the waypoint parameters. Once finished, click on the transmission icon to send the mission to the vehicle.
The altitude indicator on the bottom provides a sense of the relative altitude of each waypoint.
Once the mission is uploaded, switch to the flight view. It generally does not allow to modify the mission, but is optimized to track its progress.