To modify the EmulationStation menu mapping, edit the file /recalbox/system/.emulationstation/es_input.cfg. In the 'deviceName="Keyboard"' section, set the 'id' property of each input to the SDL keycode for that keyboard input. To map virtual gamepad button "a" to keyboard key "1", locate the input with 'name="a"' and change the value of 'id' to "49".
<input name="a" type="key" id="49" value="1" code="168" /> <!-- gamepad a ==> keyboard 1 -->
[EDIT] In this example, the SDL keycode for keyboard key "1" is 49. SDL keycodes are listed here - https://wiki.libsdl.org/SDL2/SDLKeycodeLookup.
