This is in magento 2.1.3
I have a bunch of simple products imported, as well as the configurable product that is supposed to be imported.
At first I could not find the link to "add products manually" under configurations. Then I read that you have to first add a configuration through the wizard for that option to show.
So I added a fake configuration through the wizard, and then I am able to associate the simple products. I click save on the configurable product, and then the simple products that were added disappear.
I know this whole system seems a little finicky right now, but is there something I am missing that would make it work?