Les, to my understanding - DNN 5.x documentation is way off than the actual functionality. Documentation is not up-to-date at all. One has to play, experiment, and struggle to figure out what changes are made and where exactly are the control and check points. I am with you on this.
When you go to "Host->Extensions" you are able to see all the extensions, and also this is the place where you set the extensions for the entire DNN installation. While "Admin->Extensions" is the place where you set the "extension properties & options" for the specific portal.
Again, to my understanding, for integrated windows authentication, you will need to install "AD Authentication Provider" (Host->Extensions - scroll to bottom - on bottom right click "Install Available Extension" - then install "AD Authentication Provider").
Once you install AD Auth Provider - then you need to configure it to do this click "Admin->Extensions" then click on the "Edit Pencil Icon" next to AD Auth Provider and then configure it to work with your setup.
Me no expert on AD - so refer AD Auth Provider forum under "Authentication Providers" forums.
Hope that helps,
Good Luck,
Sincerely,
Sid