I thought the pop-up flash communicated with OCF's via different pulsed flashes... Wouldn't covering it up prevent it from doing this. You can just set it to master mode and change the output to nil like YoMoe ^ said.
It does, but the pop-up commander does this flashing (communicating) before the shutter is opened. It will still do that communicating (flashing) even if you disable the flash contribution with its mode "- -". The "- -" just means the internal flash will not contribute to the scene lighting as another flash unit. It is still commander however (before shutter opens).
One big problem is that all this flashing before the shutter opens turns out to be pretty well timed well to make the subject blink their eyes, which the following picture probably will capture a picture of.
The SG-3IR shield - or the infrared SU-800 commander - (both filter the flashing to allow infrared light which works as the communications, but blocks the visible light that the subject sees) can minimize this visible flashing and blinking. However, the remote TTL flashes still respond to the commands with their visible flash, and they will flash their TTL preflash for the TTL camera to meter. These remote flashes are less centered in the subjects vision, somewhat less problem, but not at all impossible they may still blink.
A better scheme would be to learn to use FV Lock (on cameras with a commander). This is probably a programmed function button on camera, and pressing it causes all the early command flashing, and also the TTL preflash from the remotes, and the metering (the Flash Value). It does not activate the shutter however. So the subject probably blinks, but no shutter to take their picture. Then in a few seconds, you do the shutter button (possibly multiple times), to take the picture(s) using the remembered Flash Value previously metered. No extra flashing, no subject blinking. Using FV Lock is an excellent solution, virtually mandatory for pictures of people. FV Lock is only necessasry if a remote flash is TTL mode. Nothing happens at FV Lock if all remotes are set to a manual power level (nothing needed - the commander menu already knows the power level they will use).
Even the hot shoe TTL flash (no commander involved) does the preflash, and some few sensitive people will always blink then. FV Lock solves that too.
One other issue though. After the shutter does open, the Commander must flash one more command that tells all remotes "OK, Everybody Fire NOW! This is a weak flash, normally little problem, but it can cause a visible reflection in close or reflective subjects. The SG-3IR panel can greatly minimize that too. In fact, it is designed for close macro work.
See
HERE about this trigger signal and the SG-3IR panel,
and right above it, see
HERE about FV lock (on cameras with a commander).
This is one issue about putting a SU-800 commander on a camera model without a commander ... still no FV Lock. It could be argued that it needs it less.
