How does one go about programming the 16u2 on an Uno? I have the isp header (for the 16u2) hooked up to another Uno programmed as ArduinoISP I'm not talking about DFU or USB->UART, I'm talking about using it like a standalone chip (Like, say, a Leonardo or Yun [the 32u4, not the Linux, obviously])
First you need to write a program for it. There is no Arduino core for the 'XU2, so you will need to write it out longhand. Then you compile it. Then you upload it using ISP. Then you run it. Note that the only pins you have access to on the board are the UART pins, the two on the LEDs, and the 3 on the ISP header.