So I’m having hard time figuring this one 
I’ve mapped my Arcade Stick controller for fb_alpha_libretro to match the layout of the CPS3 system :
LP MP HP - LK MK HK -
But when I want to play some Neo Geo Game it’s all messed up :
C D - - A B - -
Instead of :
A B C D
Is there some way to setup the controller for each game or each system (MVS, CPS3, etc…) ? Other than change the Core for each system ?
After some research, some people are saying that you can setup your controller per-system like this :
retroarch\configs\SYSTEMNAME\retroarch.cfg
The retroarch.cfg file would be generate from the RGUI as “Save new Config”. Find the file created, rename it retroarch.cfg and place it in your SYSTEMNAME folder.
But it doesn’t seems to load… In my case it doesn’t work though.
What if I can call it via the command line in es_systems.cfg ? What option(besides -L) do I have to write ?
<command>D:\Games\EmulationStation\systems\retroarch\retroarch.exe -L D:\Games\EmulationStation\systems\retroarch\libretro\fb_alpha_libretro.dll "%ROM%"</command>
Didn’t try it yet but is there some sort of wild card that can let you load your custom config.cfg like %ROM%.cfg
That way we can load it per-game ^^
Yep there is a wild card ^^
Custom Config Per-System you go like my post up there :
<command>D:\Games\EmulationStation\systems\retroarch\retroarch.exe [B]--config D:\Games\EmulationStation\systems\retroarch\configs\customconfig.cfg -L [/B]D:\Games\EmulationStation\systems\retroarch\libretro\fb_alpha_libretro.dll "%ROM%"</command[B]>[/B]
Custom Config Per-Game you go like this :
<command>D:\Games\EmulationStation\systems\retroarch\retroarch.exe [B]--appendconfig[/B][B] D:\Games\EmulationStation\systems\retroarch\configs\[/B][B]%BASENAME%[/B][B].cfg -L [/B]D:\Games\EmulationStation\systems\retroarch\libretro\fb_alpha_libretro.dll "%ROM%"</command[B]>[/B]
Pretty handy for Neo Geo games where you play with a lined-up buttons layout for shooting or puzzle games and switch to square button layout for fighting games. Or when you have a “Retrogaming” category with multiple systems inside 
Works great with fb_alpha_retro.dll. Didn’t try with any other Core.