I have to admit that I made one fundamental misconception some time ago: I thought that I can't activate my Nikon SB-600 without flashing the object with my pop-up flash. After all, even when I set the intensity to "--", the pop-up flashes to control my slave.
But: It flashes before the exposure starts thus it doesn't affect the picture. It kind of just tells the external flash: "Pls flash in 0,0123424532 seconds, KTHXBYE." And the external flash obeys, after all that's what you slaves have for.
So to state it even more clearly: In order to make a classical nice 1 strobe-through-1-umbrella-picture you just need a reasonably modern Nikon flash (SB-600/800/900), a middle class Nikon cam (eg. D90, alternatively add a SU-800 commander to the equation) and a light stand. Set the pop-up flash to master in menu e2 and there you go: You can control the power of the pop-up flash (I strongly suggest "--" for off) as well as the settings of the off-cam flash from the cam. How convenient is that!? It doesn't matter whether you use iTTL or manual mode, it's all there, on your camera display.
More about how to use the AWL/CLS, make sure to read Ken Rockwell's introduction. For a general introduction to off cam strobing is one great place in the Internet: Strobist.com.
P.S. Why use AWL and not cheap radio triggers? My killer argument is "FP" aka fast-sync: It facilitates to flash at much faster shutter speeds than 1/200s. The downside is still that you have to ensure that the light from the flash reaches the infrared sensor of the external flash at the side.
Update: As zhx points correctly out, there is some light spill from the pop-up flash. You can easily test it by shooting into a mirror. However if you keep some distance, there will be no visible traces of it in the exposure.