Hi Mike,
As you discovered, the Marker is for temporary use - it's not saved. A common use is to track your distance to a point on the map, since that value updates as you get close. If you touch the white area of a marker it will go away.
You also have the option of creating and managing Custom Waypoints. Touch the map and pull up the Possible Actions Menu, then touch "Add Custom Waypoint". The Custom Waypoint will be created where you tapped the map. It will have a default name, but you can touch "Rename" and give it a friendly name.
You can review & edit your waypoints by touching Menu, Custom Waypoints. Also from here you can toggle whether these are always shown on the map or not.
Hope this helps,
Walter