Running script inside sandbox

Hi I'm a little confused about how to customize my ZAV apps. I need to run a script to update a registry inside the ZAV app sandbox, and then run the actual executable, can someone point me as to how to do this?

I put a cmd file in with the installation before I compared the snapshot it, but the commands actually interacted with the physical host and not within the sandbox like I was hoping.

thanks

Wil