If you are capturing the trigger flash, which occurs while the shutter is open, you will need to use the SG-3IR or an IR filter over the pop-up flash to block the visible light. You could also use the SU-800 which provides IR only control.
The Nikon AWS system uses IR, Infra Red, light to communicate and control the remote units. The pre-flashes trigger each group individually for computing the exposure before the camera's shutter is opened. There is a trigger flash after the camera shutter is opened, synchronizing all the flashes to fire while the shutter is open. See "New CLS Preflash Sequence Images" for a lengthy and sometimes technical discussion bout how the AWS system works, flash sequences, timing, and coding.