Layered document etiquette
Layered Documents by nature are harder to get an overview of, so you should know how to create easy-to-read, clean documents. The default, stock smart materials in Painter are seen as a good example of clean, readable materials.
Documents should be structured in a way parallel to how they are created in real life. Every material that would be physically separate in the real world, should have its own Layer Group and Mask, with proper naming (be clear and descriptive). The order of these materials does not matter (if masked properly).
Global effects such as dirt, dust or adjustments and corrections should also each be placed in a separate Layer Group, mostly at the top, or in the correct position dictated by the document.
It is a huge help to use Layer and Group Coloring by right clicking in the Layer Stack and choosing a preset layer color. Assigning different colors to different Layer Groups makes a document much easier to navigate through when Groups are left expanded.
The goal is for someone to be able to open a document and quickly be able to tell different materials and effects apart.
Layers within a material group should be placed in a logical, top-to-bottom way. For every standard material, there is one Fill Layer that sits at the bottom named "Base", just like the default Smart Materials. Any other effects are then layered on top of this Base Layer.
Avoid Duplication and Duplicate Names
Duplicating a Layer or Layer Group without much modification is not a good practice and should be avoided. If you can, use Passthrough Blend mode or Anchor points instead.
Be aware that if you do duplicate a layer, naming should always be changed: layers named "Layer 01 copy" are bad practice when shared with others.
Normal / Height Blending
Blend modes make a big difference in how Height and Normal channels affect the final result in the viewport. Default Blend modes for Normal and Height are set up to mix and Blend these channels, not to override data below them. Change these if you don't want Height or Normal info from materials to "bleed into" each other. Be aware that the Blend mode of Layer Groups also affects this, and is best changed for smart materials.
Avoid old or unused Data
Leaving Old or Unused (visibility toggled off) Layers and Groups in a document is bad practice. If it is really necessary, these layers are to be marked "Old" or "Unused" in naming, and have layer colors set accordingly. For example a Layer Group named "(OLD) Dust Effect", visibility toggled off and colors assigned to gray.