The steps above are prerequisites for the deployment as a whole. In the tool you need to configure it to have the same settings as your deployment.
So as an example,using header authentication (recommended) :
If the value of the prefix field in QMC is "header" you set VirtualProxyPrefix in the tool to "header".
If the header authentication header name in QMC is "QlikSenseUserHeader" you set the HeaderName in the tool to "QlikSenseUserHeader". If you are using https, then you need to check SSL in the tool and you might also need to check AllowUntrustedCertificate. If you don't check SSL in the tool you need to enable http in the QMC.
Of course, you also need to input the App name (guid or friendly name) and the server address in the tool.
To check that your settings in QMC are correct the best way if to test accessing the app manually using the header. Firefox+modheader plugin is a good way to do this. This means you need to have the header prefix in the url and also send in the header as stated in the QMC with the plugin.
To check whether or not the tool is configured correctly the best way is, in the tool, to click "App Structure" and connect to app in the tool. Getting the App structure is also very helpful when you are creating the scenario.