First of all... I hardly ever see the need for layers in NX, not when you can simply 'show' or 'hide' entities or groups of them in the Part Nav. Layers are an old 2D CAD system carryover and while some still use them... I've found limited use for them in NX.

You can think of this way if it makes it easier.... Reference Sets for parts and Arrangements for assemblies.

Here's an example that I work with almost daily; a complex gas turbine engine part that contains not only the sheet and solid bodies but numerous build planes, datum points, axis, etc.. Open one of these with everything shown and it's an utter mess to deal with.

It is much easier to deal with these models by creating Reference Sets. Let's say, the "Model" Reference Set to contain the final single solid body. Another Reference Set called "Model + Datum Structure" where the model plus all the pertinent datum are selected. Maybe another Reference Set called "Wall thickness inspection" that carries all of the technical data (points on the surface) where the airfoil is to be inspected.

With the creation of these Reference Sets, you can choose the best one for your assembly task upon adding the model to the assembly.

Arrangements allow you to create let's say.. a clamp in 2 different positions; "Clamp Open", "Clamped Closed", etc.. Switching between the assembly's arrangements then updates the model/assembly with constraints specific to Arrangement. Can also be used to "suppress" or "unsuppress" components per the chosen Arrangement.

There are other possibilities but, these are the basics.

Then there is Promote Body and Wave Link body, which can be useful for pushing a body to the Part Navigator, where it can be modified within the assembly... without affecting other places the component is used.