My 2013 Cc (under 20k miles) is out of alignment on 3 corners. I'm trying to find a repair shop that has the software to fix it since I think that'd be cheaper than the dealership.

Hitting any type of pothole can knock one out of alignment. There should be plenty of small garages around you that have the machine to take care of it for you.

Being a CC owner and a VW sales consultant I would advise not to skimp because of price on repairing your car. Take it to VW service and have the guys that are tech trained on the product instead of some shad tree outfit that does not know the workings of the vehicle. I would get up with your sales consultant (the guy who sold you the car ) and go through him. I fhe is a good consultant he will have a working relationship with the service department. and can speak in your favor. Even so, any major repairs should be covered in the warranty if under the miles stated in your purchase contract.