Purpose: How to Deploy an Application with User Settings (HKCU) in SCCM 2012
Many applications contain settings only for the current user (HKCU). There is no way to replicate these settings for the local machine (HKLM) as the program is designed to read the settings only from the current user registry or current user profile documents (%APPDATA%). Now in corporate environment, you can use group policies, logon scripts, and such to manage your user based settings. However, if you want to keep all of it in the SCCM, there is a way for you to do it.