1. Copy retroarch.cfg and name it the system you want to change the config. For example, lets say “Atari 2600.cfg” This has to be named exactly the same as the system name.
2. Now place your newly created system config (eg: Atari 2600.cfg) into H:\HyperPC\Emulators\RetroArch\config
3. Now launch AM, select your system then a game.
4. When the game is launched press F1. Go down to Configurations and it “should” show that its now using the system config (eg: Atari 2600.cfg) and NOT retroarch.cfg.
5. Now any changes you make will be reflected in the system config and not the main retroarch.cfg
When you are in the game, Press F1 and go to the quick menu, controls, set your device type (try retropad and also retropad w/ Analog, some controllers need retropad set, some need retropad w/ Analog) and click save core remap! I believe save core overrides will work as well.