Are you asking if you should set the D-700's built-in flash to commander mode? Are you using the SU-800 that's part of the R1C1?
If so, the SU-800 is controlling the remote flashes and the built-in flash is not used at all. How you set the D-700's flash doesn't matter. If you dial in flash compensation on your camera, that will affect the flash output.
If you are still planning on using the built-in flash, perhaps because you want want it to contribute to the lighting, or because you actually have the R1 (no SU-800) then yes, you want commander mode in the D700, and you do not use the SU-800, if you have one.