Jason - Nikon has a system called Nikon Creative Lighting System (CLS) that allows multiples flashes to be used off-camera without additional triggering hardware. This is what you want to be tapping into...
Basically, the on-camera/pop-up flash sends out a series of pre-flashes (just before the main flash used in the actual exposure) and these pre-flashes tell the flash what to do.
You want to refer to page 58 onwards for how to set this up. When it comes to setting the pop-up flash as your commander flash (the one that commands the set-up) set it on the '--' setting so it fires the pre-flash but doesn't really add to the main exposure. You can get shield that go over the pop-up flash to cut out any stray light.