Hi Steve,
Thank you for your response. At this time, there is no way to navigate through emails when they're viewed in the popped out window. I know there are other clients that offer this functionality, and I can see how it would be useful. SmarterMail's interface will be getting a drastic facelift in 16.x; I will be sure to suggest this functionality.
I'm going to change this thread from a Question to an Idea so we can facilitate tracking on the request.
Thanks!