Have you tried using emuloader? supermodel UI isn't ready to configure the neser versions of the emu, and it also creates a bunch of stuff in the supermodel.ini file that makes it really messy.
Anyhow, have you thought of editing the supermodel.ini file yourself? The options are pretty well separated in parragraphs and pretty clear in explaining explaining what everything does. I don't know the names for configuring the buttons of an X-input device (such as the xbox controller), as I use a Logitech controller that uses Direct INput, so the naming may vary, but I think you'll find you have more control over stuff.
keep in mind that you need a fresh copy of supermodel AND the ini file, because supermodel UI fucks the ini file beyond any recognition.
I know that you are using an xbox controller, so you should enter supermodel.ini and look for
[ Global ] ;
There are some options for choosing your graphics engine here and stuff. To use an xbox controller, you have to add this line:
InputMethod = 1