I’ve tried the steps in 3.b.1. Adding Devices to Atmel Studio 6, but in the path C:\Program Files (x86)\Atmel\Studio\7.0\tools\STK500 I don’t have the xml folder
It looks like the AT32UC3C0512C can only be programmed through its JTAG and aWire interfaces. It does not have the AVR ISP interface that is used by the Pololu USB AVR Programmer and the Pololu USB AVR Programmer v2, so you will not be able to use either of those programmers with it. You might consider using the AVR Dragon instead.