Option 1: https://xenappblog.com/2013/customize-windows-2012-start-screen-using-group-policy/ – export the layout, push it out via GPO to all users. Unfortunately, on Server 2012 R2 this means users can’t modify the Start Menu after this.
Option 2: http://microsoftplatform.blogspot.ae/2012/11/predefining-and-customizing-modern-ui.html – much better. You push out a default “template”, but users can customize it further on.
On a related note: http://virot.eu/push-a-solid-colored-background-to-a-windows-server-2012-or-later/ – for customizing the Start menu colors (these are the colors of the background you get when pressing the Windows button on Server 2012 R2. I find it better to modify the colors first so the two registry keys mentioned in this link are created).