I've never really used Linux but logically speaking the simple automation of renaming in-and-out of multiple config files based on certain basic triggers or conditions shouldn't be rocket science on any OS. Or do you mean more than one config running against one single instance of cgminer?
I think it is possible to have 2 config files with 1 instance of CGMiner or just running two instances of CGMiner. I was advised strongly against it and told to just use two Raspberry Pi's.
To a lot of people (non computer experts), scripting and sysadmin is a lot like rocket science. I'm an EX-IT expert, and honestly, it is just a headache even when you kinda know what you are doing. These miners pretty much run, but adding complexity in the way we are talking can be a real big headache when problems are experienced. I've worked on computers for years to know otherwise. Just trying to save others the headache.
I would STRONGLY suggest to people non fluent in sysadmin work / scripting to not even attempt to run two config files or two instances of CGMiner on one Pi.
Running MinePeon with it's GUI interface is about as far as I would suggest a Semi-noob to go. And even then, they have to know a bit with regard to Linux commands to get around. At a basic level just setting up the Raspberry Pi remotely (no monitor connect) can be a headache.
IAS