Why are you attaching SB-900 with sync cord? Which sync cord is it--a regular cord or a NIkon TTL cord? Optical triggers don't have much more range than CLS does, and you have to be careful what kind you get. The older style will be set off by the iTTL preflash. Also, to use optical on SB-600 you will need to buy a hot shoe with PC connection. If you are just just using flash and camera in M mode, buy some radio triggers such as RF-602. Apparently there are new radio triggers coming out very soon that also support iTTL (TR-331, not JrX or PW, something newer and cheaper.)
If you're using a Nikon TTL cord to link the 900 to your camera, you should have full control of both flashes from the SB900. I use a similar set-up frequently for studio product work, and it works fine. The only problem is having to set the flashes from the SB 900 which is remote from the camera. If you're using only two flashes, it's much more convenient to use the pop-up flash as the commander--then you have full control of both flashes from the camera. The only time I use the commander flash off-camera on cord is when I need to control more than 3 groups of flashes.
Oh, crap--you're shooting one of those crappy D3s with no pop-up flash--guess you're stuck with it!
A sync cord is all I have for off camera. I bought a pc sync cord from flashzebra. I have two
softboxes and two flashes.... No popup commander flash on camera
I didn't think it would be hard to fire both flashes in manual mode. The 900 fires great with the sync cord....
Yes, the 900 fires in manual just fine using the PC cord, but it won't work as a commander. Break down and spend the bucks for an iTTL sync cord, and your problems are solved.
Being able to control multiple flashes in any mode from a single unit: Priceless.
PS: If it's possible to use the SB600 in SU-4 wireless mode, then you should be able to use it in manual or non-TTL auto with the SB900 on a PC cord as the trigger flash. The SU-4 mode mimics an old-school light slave: It fires the flash when it sees another flash.
