On my D200 / D300 I did as most others have reported, matching A,B,C and D definitions on both banks. Mine were set up for General, Macro/tripod, Landscape and Wildlife/action because those are my main interests. I found I was frequently making adjustments to my 4 groups in both banks of settings to compensate for day to day variations in shooting conditions.
When I got the D800 I decided to think a bit more deeply about the reasons for Nikon's design team splitting the settings into two banks. My reasoning was this : Four groups of settings (A,B,C,D) give you 4 different virtual cameras in one. If you could find independent intentions for each of the 2 banks of four, you get a matrix of 16 virtual cameras. (for the non-mathematical people any of the 4 groups in Custom Settings Bank, paired with any of the 4 groups in Shooting Menu gives up to 16 unique combinations) This must have been the intention of the designers - to maximise flexibility - so it stands to reason that they would have grouped all the available choices into logically independent groups.
Looking at lists of the settings you can see this is actually the case.
The Custom Settings Menu relates mostly to things you do with the light that enters your lens, physical camera controls and choices that you make in preparation for the photograph (i.e. before the shutter opens) such as : - method of acquiring focus for different types of subjects - exposure and metering - timers - release mode, mirror delays etc. - flash
Shooting Menu consists largely of choices relating to the processing of image data captured by the sensor during and after exposure, such as : - colour profiles (picture profiles) - ISO sensitivity - Noise reduction - D lighting - White balance - Distortion control and Vignetting - File naming, image quality
Consequently I am experimenting now with banks set up as described below : Custom Setting Menu : A = General Purpose Handheld B = Landscapes C = Wildlife / Action D = Macro
Shooting Menu : A = Normal, Good Light (limited Auto ISO range to maximise IQ) B = Low light, Handheld ( allows high ISO settings, forces faster shutter speed, enables D-lighting to bring out shadow detail, disables LENR) C = Low light, Tripod ( restricts ISO, allows long SS, enables LENR) D = HDR (Just for fun, HDR with Vivid picture profile, high contrast and sharpening)
These settings allow me to match prevailing lighting conditions to any of my favourite shooting genres by making just 2 menu choices before I start shooting. After that, virtually all further adjustments made during shooting are done with the physical controls (buttons and dials).
I am still fine tuning the Auto ISO settings in particular. I hate ISO noise and I also hate the hassle of applying NR in PP - so rather avoid getting noise in the first place.