'Save settings' saves most of the camera's settings (including Shooting Menu Banks and Custom Settings Banks) to a CFe or SD card.I'm unclear on exactly what you are saying, are you saying that the "save settings" is needed to save bank settings once you set them? I don't recall reading that but my memory is faulty at times. What I got from Patrick's message is that the "save settings" saves the individual bank settings, but then sometimes I read too quickly! According to Nikon the "save settings" is only to put them on a card...
My practice is: Enter the settings I prefer in each tab in the Menu (Photo Shooting thru My Menu). I keep track of these settings in an Excel spreadsheet (an expansion of the one Steve provides). Over time, I change these settings somewhat as I evolve in my use of the camera. Regardless, once the settings are entered in-camera, I save them to a card using 'Save settings.' At the end of a day of shooting it's likely that I changed some settings due to weather, lighting, etc. In order to ensure that the settings are reset to my defaults for the next day's shooting, I load my saved settings from the card. When I pick up the camera next, I know how it's set up and I go from there. Not everyone does things this way, but it works for me.