Simple, you don't. The only thing you can do through the NowTV app is pay to watch Sky movies.
Consider adding a NowTV box and a Sky Entertainment pass which will get you live access to all the Sky entertainment channels and catch-up.
I use this option since I moved to BT from Sky and the only thing I now miss is the Sky F1 channel.
The only way you can watch sky Atlantic is on now TV entertainment pass all 11 channels including sky one that you have to register with their TV that you have to register with their There now TV online .
If I get the now tv box does it not let me watch Sky Atlantic without buying a Sky subscription
That's correct. Nowtv boxes only allow you to see Sky's entertainment or movie channels if you sign up for one of their passes. Nowtv is part of Sky.
AFAIK the only way to get Sky Atlantic is via a Sky or Nowtv subscription. That's one of the channels Sky don't let any other providers supply...