AF assist from the flash is enabled when the the following conditions are met: 1. The flash is on the camera. 2. AF Illumination is enabled on the SB-600 through the SB-600 custom settings. 3. AF-A or AF-S is selected. 4. A valid focus point, as described on page 279, is selected.
The Flash Commander has nothing to do with AF Assist, and AF Assist cannot be used when the flash is being used as a wireless remote. The problem is that the AF-Assist light has to be on the camera.
For wireless operation, the SU-800 Wireless Flash Commander has an AF Assist light built into it.