PCBnew handles the libraries differently than EEschema, their format is also completely different.
EEschema will converge to that same system with KiCAD v5 afaik (or not if the newest rumor is true 
).
With that being said, current state of affairs in KiCAD v4..
PCBnew:
- libraries are
.sweet.pretty folders - footprints are .kicad_mod files
- .kicad_mod files contain all information for that footprint, even the link for the 3D model
- configuration is stored in fp-lib-table file in your KiCAD settings folder
- fp-lib-table can be modified using the Footprint Library Manager (via CvPCB or PCBnew)
- fp-lib-table can handle environment variables, to make library management easier
- is able to load libraries from github
EEschema:
- libraries are .lib files
- symbols (components) are entries in that file
- additional info is stored in .dcm/etc. files
- library configuration is stored in the projects .pro file (and globally in the template kicad.pro file, located in the KiCAD program folder in /share/kicad/template)
- the project libraries settings can be modified via the Component Libraries dialog (from EEschema)
- to change global settings (for projects you start new only, as they load the template.pro file to start, existing projects don’t do that) you have to locate & load the template file (kicad.pro), adjust it’s library settings and then save it
- can’t load libraries from github
Also of note a quirk for loading symbols:
- if you have symbols with the same name in different libraries, EEschema will always and only load the one that is in the library that comes first in the list of libraries