Mixed controllers not working with LR-Stella

[generatorlabs]

My scenario is very basic.
I have a USB to Atari adapter. The adapter did not register the Axis values correctly so I followed another blog that had me compile a new current Kernel. After a few hours I was able to see that the adapter was now working.....Hurray!

So now I have two functional controllers. I have a wired x-box controller and my Atari controller.

I have tested Stella with both controllers. They both work. The x-box controller will let me set up hot-key&exit controls.
Unfortunately I don't want to play Stella with that type of controller. I really want to use the Atari controller for gameplay and use the x-box controller for secondary functions (ie Exit).

I cannot get both controllers to live in harmony. Is it not possible for Stella to see input from more than one joystick at a time?
On my keyboard CTRL and ALT will exit Stella. I tried mapping those keys to buttons in the Retroarch GUI for the X-Box controller but no dice.

Any ideas? I don't want to have to use the Pi with a keyboard tethered all the time.