So have you performed the TEST jumper procedure to load the SAM-BA loader onto device, right?
The SAM-ICE/J-LINK JTAG connects to a PC (desktop/laptop/netbook) via USB.
http://www.atmel.com/dyn/products/tools ... ol_id=3892To do any kind of development/debugging on ARM devices you'll need a JTAG debug pod. The evaluation versions of Keil or IAR will work with the SAM-ICE, and support up to 32 KB of code. I'd recommend you try these and get an understanding of the process first, before switching to open-source tools, as the integration makes them easier to use.
For Vista I would be tempted to download the 2.11 version of SAM-BA
http://www.atmel.com/dyn/products/tools ... ol_id=3883