The first step is to find out if your controller is at all recognized by the MiST. Plug it in, turn on the MiST with an 8-bit core, then open the OSD (F12 or middle MiST button on the front panel) and go to the Joystick 1 test screen.
Is this any 8-bit core? I tried it on the NES core, and couldn't find the menu there. Is there a particular core that has this configuration option that I am missing?