I might not explaing it well but each emulator has its own file for the configuration of buttons and a file of the configuration off all of them.
I believe its located in
/opt/retropie/config

In there you will have a folder for each emulator and within the folder a file called retroarch.cfg . just put in the nessessary inputs in.

I haven’t tried this my self but I would think this is how it would work!