After I did my TT and pointed the Dana 60 to the Atlas, I filled to the hole. But it didn't look to be enough, so I jacked up the right rear tire about 8" and filled it up some more. No issues in 70k miles later.
I have a raised fill plug, but I made a dipstick to make sure the oil is at the right level (bottom of axle) when vehicle is sitting flat. IMO, it's the only way to match the factory fill level.