It's that that things are in slightly different places on the Pebble v2
Connect the board to your computer via USB. Put a jumper between the two left-most pins on the group marked "8u2 ISP" (it's near the left side of the board). Stick one end of a wire in a "GND" header, and tap on the left-hand "Boot" pad (it's right under the 8u2 ISP header). Remove the wire, remove the jumper, you should now be in DFU mode.
From there, follow the normal "dfu-programmer" instructions.
(Note if you want to build any LUFA-based projects yourself, you'll probably need to use LUFA 100807 rather than the latest version - I got weird build errors until I rolled back).