Markers are little notices ingame to help you and your alliance members communicate. They can be created by anyone in your alliance and only seen by people in your alliance. Only the leader and minister can edit/delete markers (see Alliances).
How To Create an Marker
Go to your orders menu, then go to the alliance section and click create. After clicking create you will see a pop up window where you can choose the type of marker it will be, the place it will be put, what the name of the marker will be, and the description of the marker.