Upgrading your installation: If you have a System Center 2012 R2 Configuration Manager installation, you can use the System Center 2012 Configuration Manager SP2 media to install the latest patches and automatically upgrade to System Center 2012 R2 Configuration Manager SP1.

New installation: Install System Center 2012 Configuration Manager SP2 first, and then install System Center 2012 R2 Configuration Manager SP1 at the top-tier site of your hierarchy. Both of these installation files are included on VLSC.

PS:
Don’t forget to install the latest CU1
https://support.microsoft.com/en-us/kb/3074857