It would seem that the eval boards should come with debugger targets already installed. I would expect that connecting an Eval card to a PC with software you should be able to download and execute code. It would be nice to download over USB or Ethernet. And it seems that a JTAG ICE is needed. Not ideal, but OK.
Got the EVK1100, Atmel-ICE and the extra kit with the 50mil to 100 mill adapter (thanks). Set up Studio 6 and built the EVK1100 demo application (confirmed build worked with the simulator). Selected Tools- Device Programming, selected JTAG-ICE and clicked Interface 'APPLY' (bit tricky there). Did a fresh build and clicked 'DEBUG' 'START Debugging'. The debugger cycles a bit and reports "Error: Saving to device failed".
Poking about on the net suggests that the ICE is having a hard time talking to the target.
Any suggestions on where to look next?