I will give it a go, but don’t take this as canon:
es_input.cfg will define your controls in emulationstation (the gui you usually use to select the rom/system you want to launch). From what little I understand, any commands here will get passed to all libretro emulators. If you delete it, emulationstation will create a new one the next time it is launched, asking you to define the controls for any devices attached.
/configs/all/retroarch.cfg sets global configuration options, like display options, sound options, default emulators for each system, hotkeys and anything else you think about.
Note: the cfg file on each emulator directory will override these configurations for that emulator only.