I think under the CLS menu you set the internal flash to off (--) and the SB800 to whatever you want to set it to.
Pop the internal flash up, it'll fire for the communications but not fire for the actual exposure.
That said, if you're photographing something very near, you might get some residual glow from the flash tube having just fired.
The alternative is to get an SG-3IR, which goes in the hotshoe and covers the built in flash with an IR filter. That or tape a bit of unexposed but developed black and white film over the flash. Those are more for when using the optical trigger than the CLS system, the method above should work for you.