In Tools folder you have a tool called WorldEditor. All the stuff you want to do, you can do with this tool.
To remove location, double click a location on the map and click "Remove from Worldmap".
Adding locations: also in WorldEditor. Ctrl + A, choose the location and click on the map.
Don't forget to File -> Save to save the changes.
If you already run a server, it won't delete existing location on the server, but you can remove it in the game with admin command.
