66 - Layers of Structure are restrictions you place upon your workflow or tools that add order, which in turn creates repeatability. Repeatability is important for effective note taking because it allows for a greater amount of applicability per note. This is the same idea behind creating connections between notes and keeping notes atomic.
Once you get a sufficient amount of layers of structure together then they make up a workflow or system such as zettelkasten, PARA, or IMF.
Same applies to tools such as Obsidian, see 15 - Obsidian Enhancements. You start off by writing on wood and work your way up to complex mediums such as books with developed finding devices.
16b - Layers of Structure in a Wiki