You can manually upgrade by browsing to .\Config Mgr Installation Folder\tools\Console Setup and execute Console on each computer running the console. This method gives you more control on the group of computer you are upgrading.
We suggest to create a package or application pointing on the same directory and deploy it using a collection. I like to create a collection that targets clients the latest SCCM 2012 R2 SP1 version.
If you’re already running SCCM 2012 R2, the upgrade process won’t do a site reset : From Technet: When you run this upgrade, it enables additional capabilities throughout your hierarchy.See the full list of features on this Technet Article to figure it out.Following the announcement, the community was confused on how to apply this Service Pack because Microsoft decide to release it under one binary even if there’s 3 possible “version” of SCCM 2012.Just replacing the old image with the new one on the filesystem is not enough.If there is a way to import/renew/add new boot image in SCCM try it.