Hi,
I'm not sure what kind of configuration you are using for your installation package, therefore I can suggest two methods (you can choose the one that is best suited for you):
1) in the "Organization page you create features and include the components of the registry key in one of them
2) you condition the installation of the components of the registry keys in the "Organization" page
You can read more about the "Organization" page here:
http://www.advancedinstaller.com/user-g ... ation.html
If you need more information about this then please give me more details.
Regards,
Cosmin