The front and back covers of your publication will be aligned in the centre, or to the right/left of your screen depending on the way you supply your files.
If your pages are in a portrait orientation and you upload them as single pages, the front cover will be aligned to the right, and the back cover will align to the left of your screen.
eg: http://garvan.realviewdigital.com/?iid=89671
If your pages are in a portrait orientation and you upload them as double page spreads, the front and back covers will be centred. However, this will effect the apprarance of your publication on tablet devices when held in portrait mode - as the double page spread will always be displayed.
eg: http://iconic.realviewdigital.com/?iid=67574
If your pages are in a landscape orientation, you will be uploading them as single pages. These will always be centred as they are designed to be viewed on a widescreen monitor or landscape held tablet device.
eg http://digital.realviewdigital.info/
