Definitely only run MAME, not MAME32. MaLa provides a GUI for setting up all the config files for the command-line MAME anyway, I think (never used it, but there's an options button next to where you point to your mame.exe file location - and it's full of the same stuff you get in the MAME32 options menus)
...
Only having two games makes things very interesting, from a front end layout perspective.
If I was doing that, I'd (assuming MaLa) make two completely isolated layouts, each customised to one game... maybe lifting graphics from the flyers, marquees etc.
I'd then create two gamelists, with only one game in each, and set MaLa to swap layouts based on the selected gamelist.
Then just make sure you've bound a button (perhaps the pedal or gearshift?) to rotate through the list of (two) gamelists and there you go - completely excellent, completely customised to your cab and idiotproof game selector!