Try editing es_input.cfg manually, add another input section for the Atari joystick after the keyboard like this:
(/home/pi/.emulationstation/es_input.cfg)
<?xml version="1.0"?>
<inputList>
<inputConfig type="keyboard">
<input name="a" type="key" id="13" value="1" />
<input name="b" type="key" id="8" value="1" />
<input name="down" type="key" id="274" value="1" />
<input name="left" type="key" id="276" value="1" />
<input name="menu" type="key" id="109" value="1" />
<input name="pagedown" type="key" id="281" value="1" />
<input name="pageup" type="key" id="280" value="1" />
<input name="right" type="key" id="275" value="1" />
<input name="select" type="key" id="108" value="1" />
<input name="up" type="key" id="273" value="1" />
</inputConfig>
<inputConfig type="joystick" deviceName="**insert Atari joystick name**">
<input name="down" type="axis" id="1" value="1" />
<input name="left" type="axis" id="0" value="1" />
<input name="right" type="axis" id="0" value="-1" />
<input name="select" type="button" id="2" value="1" />
<input name="up" type="axis" id="1" value="-1" />
</inputConfig>
</inputList>
You need to find the device name of the joystick in Linux, use ‘dmesg’
Look through for ‘Product’ and ‘Manufacturer’ relating to the joystick and edit accordingly e.g.
deviceName=”Retrolink Atari USB joystick”
I’ve guessed the axis id for the Atari joystick, if its not right run jtest:
sudo apt-get install joystick
then
jstest /dev/input/js0
(it should be js0 if not run ‘ls /dev/input/’)
Same goes for the button (select), i’m guessing you only have one to map?
Hope this works :-)