The Server Configuration Tool is available only on Windows and Linux (x86) and Mac OS in Worklight 6.1 (see the Worklight 6.1 doc for details -> http://pic.dhe.ibm.com/infocenter/wrklight/v6r1m0/topic/com.ibm.worklight.deploy.doc/deploy/c_using_server_config_tool.html )
If you can't use the Server Configuration Tool on your platform, the easiest way to get started with deploying a Project WAR file and its console is to use on of the ant file examples documented at http://pic.dhe.ibm.com/infocenter/wrklight/v6r1m0/topic/com.ibm.worklight.deploy.doc/devref/c_ant_tasks_sample_config_files.html.
Actually, the Server Configuration Tool acts mostly as a graphic front end to create and run those ant files.