I used to have a Smash TV board in my 2-player JAMMA cabinet (more of a rack of shelves, really...).
1-player was easy: I'd just use player 1's stick for move & player 2's stick for shoot.
But when I did some rewiring to try to play 2-player, using 3 buttons for each person's shoot "stick" (I know, I was short 1 button...), I'd get pretty interesting glitching. I think the hardware or the software didn't expect you to be able to shoot in 2 opposite directions simultaneously (which you can't do w/ a stick but can do w/ a set of buttons). I don't know if the emulated Smash TV will bug out or not, but if it does, there's no way you'll be able to play a heated game of Smash TV w/out accidentally giving the game impossible switch inputs...
-Jason