It's just a way of organizing the camera settings, and you use both every time you shoot. I agree it took me a long time to get any idea at all the rationale behind the groupings, and I think the ultimate truth is that it's a haphazard grouping at best.
Off the top of my head, I'd say the shooting menu controls things that affect generating the image, like exposure and converting raw data to viewable jpeg, i.e. ISO settings and Picture Control. The custom settings control how the camera works i.e. what button does what. That doesn't however paint a complete picture and I'm sure anyone could poke plenty of holes in those generalizations.
My approach is that I don't differentiate between them, and always use shooting bank A with custom settings bank A, B with B, etc. and this is how it shakes out for my kind of shooting: A = Landscape B = Wildlife C = Shapshot/Street D = Movies
This is plenty of customization for me, and I don't feel the need to cross bank A with B or C or D.
edited to add: I put the Shooting bank selection and the Custom settings bank selection together in the custom menu so I can easily change selection of both without a lot of menu diving. It would be nice to have a setting which automatically tied them together.