Hey safada,
I had a similar issue and found this to be really helpful: http://wahlnetwork.com/2015/04/06/customization-specifications/
In order to change customization settings via PowerCLI for a template, you need to apply a Customization Specification when cloning from the template.
(I don't know if there is another method that doesn't require cloning ]: )
The guy explains his workflow of changing & applying settings, and even gives you a script that implements it.
Hope this help!