The first step is to get the PGArk how you want it in single player and then upload the PGTerrainPropertiesString from your Windows\Game.ini into your server's Game.ini. Then set the map to PGARK in the commandline manager and you should be all set.
Full instructions are located here: https://survivetheark.com/index.php?/forums/topic/99062-quickie-procedurally-generated-arks-how-to-guide/
