The derailler always defaults to your highest (smallest/outermost) cog in the rear. So shift into your highest/hardest gear and adjust away. You should adjust it without the cable attached first, though, and then fine tune it once the cable is hooked up.
Basically set your high limit first, low limit second, then attach the cable, get tension set and then you may need to tweak the limits a little bit. Park Tools has a good tutorial on this.
commuter turned bike mechanic turned commuter (also a Velocity USA employee, but this is my personal account)