Depends on your controller and depends on the game. There is too much variability to have one answer work for everything.
Accessing the runcommand menu you can make custom edits on a per rom basis:
https://github.com/retropie/retropie-setup/wiki/runcommand
You’ll essentially type in the joystick values you want to override the default retroarch.cfg in the format
input_player1_a_btn = "1"
input_player1_b_btn = "2"
Etc.
You can find out your joypad values with jstest or whatever the values show up as when you configure your controller with emulationstation.
