Hi,
How to you control Atomic ?  With a keyboard?  A Cabinet Joystick Via a JPAC or IPAC? A Keyborard Hack?  or a PC Joystick?
AtomicKey , for key configuration only works with 3 first option not with a PC Joystick.
The only way to change affectation of control with a PC Joystick is to use a tool like Joy2Keys  , that converts PC Joystick input to keyboard order. 
Now, if you have a "keyboard" kind of input.  AtomicKeys should work withtout problems.
You run it, press start , then the tool prompt you for  "action" and you just have to press the key you want map to this action.
the code you see in the file , are windows key code.