Dave,
Running the SAPInventoryMgr410Deployment.exe will prompt you for server connection information and then the directory where you want to install the server to. This will put a zip file in the directory that contains the production files edited with your settings. The intent is that this can be uploaded through the Management Cockpit for the application you created.
If you are interested in setting up the Agentry in development mode you should extract the file to a temp location and import from there into the Editor. Copy all the files from the zip except for the Application folder to your app folder under the SMP3 configuration directory. You will need to edit the Agentry.ini to set the developmentServer to False. Publish from your Editor directly to the SMP3 app directory.
After deploy/publish restart the Agentry application for it to take effect and test from the browser to verify you get the I am here! message.
All of my Agentry.ini files look ok in Notepad and Notepad++ for both Inventory Manager 4.1 and Work Manager 6.2.
--Bill