If there's a better way for things to be layed out why not learn it that way first? No reason to learn how to use it efficiently one way only to have to learn a better way once again down the road. It's not like the principles are any different.
Don't make the mistake of thinking that it's the camera that makes the photo, it isn't. It's the nature and quality of the light in which you take it. All the custom settings do is adjust the way the camera auto-exposes for various lighting scenarios. Learn about the light, how scenes look different in front light compared to side light, how they totally change with backlight, See the differences in diffuse light and strong sunlight. Get to know how this and the distribution of shadows changes and how this affects the DR and exposure. This will give you the understanding of the camera settings.
There are other settings regarding the processing of jpegs in camera and again understanding the light will help you understand their function.
I use a D600, I shoot raw in aperture priority or full manual, generally at base ISO with auto white balance. I never bother with any of the creative mode stuff, but I would suggest you learn how to adjust the AF functions and the metering modes, and how this affects the finished image first.