Earlier today the CU3 update for ConfigMgr 2012 R2 was released, containing a few nice to have fixes for ConfigMgr.
The full list of fixes, and link to request the hotfix is available here: http://support.microsoft.com/kb/2994331
Backup your Site Server
Before continuing, make sure you have a SQL Backup of the Site Server. The update will update the site server database by default.
Running the CU3 Setup
Installing the CU3 update is the same process as previous updates. You make sure you have a SQL Backup of the Site Server, and that there are no pending reboots. You can use this PowerShell script to verify prior to running the setup: https://github.com/DeploymentResearch/DRFiles/blob/master/Scripts/Test-PendingReboot.ps1. Or the update will warn you if needed, or simply reboot the site server before installing the update.
After that, simply run the setup (CM12-R2CU3-KB2994331-X64-ENU.exe) and navigate through the wizard.
Update your ConfigMgr Client Package
Since both CU1 and CU2 has been released you probably have a good understanding about how to update the client package. You can either use SCUP 2011 to do it, and/or just update your existing client package with the new files. As with the previous updates, the setup will help you create update packages that you can deploy. After updating the client, the updated components have version 5.00.7958.1401.
Update your Task Sequence
The Task Sequence components of the client or also updated which means you should configure your task sequence to install the latest components. I like to that with the PATCH command in the Setup Windows and ConfigMgr action: PATCH="C:\_SMSTaskSequence\OSD\PS10000C\Hotfix\x64\configmgr2012ac-r2-kb2994331-x64.msp"
Update your Boot images
Since the CU3 update contains updated OSD files for the boot image, you need to update your boot images as well.