Commander mode only matters in deciding which flash fires the pre-flash. So when your camera is set to Commander mode, the pop-up will fire (assuming the flash isn't shut) just before the shutter goes up (down?). This pre flash sends metering information to the external flashes with the proper power setting for them to fire.

Short answer, Yes, you can leave the camera bodies in TTL. If you are not using the SB910 as part of the exposure, it should be identical to the exposure you get using your pop-up flash to trigger the 600's (and also set not to contribute to the exposure).

Hi:
I have been firing/triggering two sb-600s as off-camera remotes using a D300 and D700 built-in popup flash with the camera set to e3 Commander mode for years. No problems. I just bought a sb-910 and I want to use it to fire the two sb-600s as remotes instead of the camera body popup flash. The sb-910 is mounted on the camera hotshoe. Ok, I set the sb-910 to "master" and everything appears to work fine (the 600s trigger) whether I set the D300 or D700 to e3 Commander mode or NOT. Can I leave the camera bodies in TTL? The sb-910 is triggering the two sb-600s whether the camera is set to Commander or TTL? But, is the exposure working like it is suppose to? The photographs look the same most of the time? thanks