Upload & Sell: On
What camera do you have? On the 7D, for example, you can use the menu to set the pop-up not to fire at all, or you can set it to fire at low power for a little fill. Regardless of the setting, it will fire a metering preflash if you're in ETTL mode, and will always fire visible command and control pulses to trigger the off-camera flashes when in Master mode .
If there are reflective objects in the frame, or if you're shooting close up, the pop-up's C&C pulses may show up in the image, but it's usually not a serious issue.
On my 7D I use the pop-up to control three off-camera flashes, one of shich is in a softbox, and as long as I'm in a fairly small room they all work perfectly. In larger spaces I use an off-camera cord running into the soft box, and use that Speedlite as the Master.
Remember that to soften the light, you have to make the light source larger in relation to the sunject; just putting diffuser material in front of it won't soften the light, it will only weaken it. Better to turn it off completely other than the C&C function so you have enough range to control the off-camera flash(es).