Hey Alley,
Your best bet is going to be controlling this at the Patch Management Agent settings within the NS console. This way you can specify specific installation, restart, notificatoin variables per group of machines as you'd like. Once you create them at the agent level than you can simply leave the Patch policies targeting all computers because the Patch Agent settings will take effect for the groups you've specified.
Hope this makes sense for you, let me know if there is anything else you need.