When you run commands like:
this tells MATLAB to create a new copy of the project. By default, this is stored in your "MATLAB Projects" directory. You can move this folder anywhere you want and make your modifications to that project. The "source" project is always within your MATLAB installation directory, so you don't have to worry about overwriting it. You can make as many new copies of the original reference application as you like, then customize them as needed.
Hope that helps,