When I was doing my research about a year and a half ago, the first seemed to be the most used one (I believe either the X-Arcade or Hotrod used that layout, whichever was around then).
Doesn't matter, anyway, I used the first layout and it works fine. I don't find any ergonomic problems when playing a one or two person game.
Eightbit it right though, hook it up however you like, and you can change it later.