Ah, when in the notification's pane. I'll wait until I have two emails and see what I can come up with.
When there is only 1, swiping side to side works to archive it. But when more than 1, it just dismisses it until next e-mail.
So, if you have 3 or more that you "dismissed", next email, you'll see 4 or more "unread" letters.
You didn't archive the 3, you simply dismissed the notification.
I want to know how to archive when there are more than just 1.
But, I won't be surprised if there is no way, but to archive it from within each message.