In the Commander, set the built-in to "--". That turns it off. However, the built-in must still send the "fire" command to the remote units, and that occurs just after the shutter opens. So you still get a tiny bit of light. Usually it's not a problem, and the worst you get is a set of catch lights in the subject's eyes. But if you're attempting certain types of product photography, such as shooting wine bottles, then the tiny bit of light from the built-in may cause unwanted reflections.
There are three ways to address this. The first method is free. Set custom setting e1:Flash Shutter Speed to 1/250 AutoFP, and then set a shutter speed of 1/320s to get AutoFP operation. When you shoot with AutoFP flash, the "fire" signal comes before the shutter opens so there's zero contribution.
The second method is to get the Nikon SG-31R IR Panel for built in Flash.
It's just a thin piece of plastic that covers the flash. It's supposed to block visible light while letting IR light through. However I've seen test results where it still lets a tiny bit of visible light through, so it may still be a problem for photographing glass.
The most expensive solution is to get the SU-800 Commander.
With the Commander you can control up to three groups of lights, and it works more reliably in sunlight. It produces IR only, so there's no visible light at all. It also has AF-Assist lights on it to help focus in low-light situations. It's nice, but pricey...especially when you already have one built into the camera.