Ok I have it now.
What I was doing wrong was tring to run ConfigurationManager.bat from a Mapped network drive.I went onto the server itself that its installed on and ran the same bat file and it worked.
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I have already deployed and started my custom workspace ear file using the application server's administration console but when I try navigate to it, it's not displaying anything for me.
Basically what I did was took adobe-workspace-client.ear and made my own custom one, just changing an image (in lc.css) to test it and called it my-customworkspace-client.ear
Within my ear I changed the application.xml file:
myworkspaceSo when I try to navigate to:
Adobe Version:
http://server:9080/workspace/ - This works
My Version:
http://server:9080/myworkspace/ - This doesn't
Hope this makes sense and someone can help!