Please add some more details about your setup, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first.
Pressing A when the game is loading and changing the resolution for the emulator. Can't seem to find the right one.
Just remove any custom resolution and leave the game/emulator running with the default resolution. Check if you haven't got a 'render resolution' configuration and remove it also.
I saw an answer somewhere to run the command sudo raspi-config. Is that the command, nothing else?
raspi-config sets the global resolution, used when starting the Pi, but it doesn't affect the individual game/emulator resolution if you're changing it from the runcommand menu.
I also saw an answer to go to Settings and choose "Adjust Resolution" but can't seem to find that.
Maybe in the Configuration Editor ?