To manage your custom map markers, open the in-game menu and change to the World tab. On the bottom of the screen you will see the commands for placing and removing map markers.
You can place up to three custom markers. When trying to place a fourth marker, it will move your first marker to the new position.
If you try to place a marker in the same position as an existing one, it will be removed from the map.
Once you reach the position of the marker in game, it will be automatically removed from your map.
Feel free to get in touch if you have additional questions!