There is no "flash off" button. There is a flash value lock (FV Lock) button. It doesn't turn the flash off; it fires a preflash to calculate the flash exposure level before the shutter is released and to lock it at that level until you press the button again.
If the SB600 is in the shoe and turned on, it will flash when you press the shutter release. The only way to prevent that is to turn the flash off.
Yes the built in flash is disabled if the SB600 is mounted and turned on.
I don't believe there is any way to use the focus assist without triggering the flash when the shutter is released.