Yes you can use the pop-up flash, SB-700/800/900/910 but they all use visible light to carry the CLS AWS IR, Infra Red, control signals.
A couple of basic facts about CLS AWS control maybe in order. IR light is part of the light emitted by all light sources unless filtered out. The SU-800 has an IR pass through filter so only the IR signal is emitted from the SU-800. The SB-R200, SB-600/700/800/900/910 and older Nikon Speedlights have an IR pass through filter over the optical remote sensor within the Speedlight.
Although the exposure test and control signals are prior to the opening of the camera's shutter, pre-release. The trigger signal only occurs after the shutter has been opened and before it closes. This is part of the reason for the need for a flash sync speed by cameras.
At the lowest possible power the visible light trigger signal from the pop-up flash will be visible in the captured image. You can purchase the SG-3IR to block visible light from the pop-up or make an visible light blocking filter from filter gels for the SB-700/800/900/910.
The SU-800 in closeup mode has balance slider to adjust the output between group A and B.