@tinybilbo Take a look at https://retropie.org.uk/docs/RetroArch-Configuration/#example-default-per-system-retroarchcfg. You'll need to edit the /opt/retropie/configs/atari2600/retroarch.cfg file (also available via file shares at \\retropie\configs\atari2600\retroarch.cfg) and change the mappings for input_player1_<button_name>.
The defaults are
input_player1_a = "x" input_player1_b = "z" input_player1_y = "a" input_player1_x = "s" input_player1_start = "enter" input_player1_select = "rshift" input_player1_l = "q" input_player1_r = "w" input_player1_left = "left" input_player1_right = "right" input_player1_up = "up" input_player1_down = "down"