How should we think of 'layers' of air flow?
To understand what a boundary layer is think about air moving above a flat plate. Before the plate and very far from it the air has everywhere the same speed and direction. However, directly on the plate its speed is zero: molecules directly on the plate do not move at all.

Between the plate surface where the air isn't moving and some distance from it where the air has a constant speed, there is a zone where the air changes its speed a lot. We call this zone boundary layer.

There isn't really any clear and distinct boundary delimiting it. That's why we have many definitions for its thickness. The dashed line in the image below is probably the 99% boundary layer thickness.



Generally we give a name to a layer when the physical effects and properties of the fluid in this concrete zone can be differentiated from the rest of the flow. Most of them are on fluid boundaries (body surfaces, places were fluids get gaseous,...) but you can have them inside a fluid too (shock waves).

For example, instead of looking at the velocity you could look at the temperature of a fluid flowing around a very hot body and define a temperature boundary layer.

Some known layers are:


Laminar boundary layer
Turbulent boundary layer
Blasius boundary layer
Stokes boundary layer
Ekman layer
Shock layer
Knudsen layer
Merged layer