Sorry I reread your question and now I can better answer it.
D90:
I will assume that the D90 is the same as the D80 in that the main flash can add to the picture AND act as the commander if wanted. From what I can gather you DO NOT want the built in flash adding to the picture, you only want it acting as the commander. All you would need to do is set the built in flash to commander mode and set say group B to SLS or a manual setting of some kind. You will then turn on your SB600 and set it to remote group B. Now the flash on the camera will only act as a commander to set off the SB600. When you fire off a photo the built in flash WILL fire, but only moments before the shutter actually actuates. That built in flash will fire but will not add to the photo, it will only tell the SB600 to fire and at what power in a few moments for the real photo.
If you do want the built in flash to add it will be firing twice in the photo. Once to communicate (act as the commander) to the other flashes and then it will fire again in unison with with remotes and your shutter. This feature is not available on the D70s for example
D70s:
The built in flash can ONLY act as the commander, thus it will never add to any photo. It is just used as a means to communicate with the SB600 and SB800s that you have set to wireless.
Note:
When using the built in wireless functions with SB600 and SB800 you will be forced to deal with lag due to the operation of a commanding flash before the actual photo takes place.