I'd suggest you check out Nikonian Russ MacDonald's blog on CLS. While I know you're doing on-camera flash, much still applies.

http://nikonclspracticalguide.blogspot.com/2008/01/nikon-flash-two-separate-metering.html

This blog really helped me to wrap my mind around what happens with flash photography.

Another good resource is Strobist. But its focus is not on Nikon and CLS, and more on just off-camera flash and controlling light. However, reading through the Lighting 101 tutorial also helped me understand what we're trying to achieve with flash lighting.