At a friends for a few days so no trusty manuals!
I have a D300 and SB600. Have CLS set on the camera and if flash is popped up, the sb600 will flash from my stand. How do I stop the camera flash flashing while the sb600 does?
The onboard flash needs to fire to trigger the SB-600 when using CLS, however what you can do is go into the menu and set it's power to "--" so that (in theory) it doesn't effect the exposure....
yes, there is, what flash in the pan said, allegedly when you set the 'built in flash' option on the camera to '--', in theory it doesn't contribute to the actual exposure.

If your not taking close-up pictures disabling the main flash (as post #4) will work fine, if your shooting closeups- Macro you can get a shadow so Nikon sell a IR filter that sits on the hotshoe to block visible light but allows the IR through to trigger the external flash, its called a SG-3IR and costs about £9