Lost on controller setup for individual systems

I can not figure this out also is there a way to check up on what is used for system’s within the system. Having never owned Atari systems I’m not as familiar with them as Nintendo. Thanks hope someone can explain this

The retropad paradigm is designed to avoid the need for remapping in most cases. You map the retropad buttons to your physical buttons and then the core’s buttons are automatically mapped to the retropad in a sane manner (usually based on physical layout).

Many but not all cores also have ‘core input remapping,’ where you can change the core->retropad mapping for that core only.