>I totally agree with Brian. The SB400 is only a little bit >bit more powerful that the built in flash.
GN of 12 meters for the built-in versus 21 meters for the SB-400, so the SB-400 can fire at 175% the power of the built-in. It also recharges faster and doesn't use your main battery.
Your profile shows that you have the 35 mm f/1.8 DX, and I'd use both lenses, with the 35 able to boot your low light capability significantly.
What I'd do:
Aperture priority mode, with auto ISO programmed for a minimum shutter speed of 1/125 and maximum ISO of 1600 (set minimum at 100), and shoot the 16-85 wide open. With the 35 mm, set your aperture for DoF, but f/2.8 or so will be a nice sweet spot. This should keep your images clean, and only rely on the flash if it's VERY dimly lit.