Could I just install another instance of CG Miner or can I do the overclock of a specific rig while not affecting all rigs?
Or would it be better/simpler to get another Raspberry Pi?
Each instance of cgminer listen on a port for commands. And MinePeon only listens to the default. So the web interface will not show both. But it's possible to run one instance "under the hood".
It would be possible to add a setting in the GUI on which port to listen and then you could switch. Maybe an incoming feature. But probably not. Buy another rpi.