Lol I hated most 2 joystick games, with the exception being Karate Champ!
Missle Command though is probably enough to leave in the trackball.
I found this thread with a layout that seems ok, not too busy but has what is probably a 4 way and a spinner at the top, plus two buttons, and the trackball in the middle.
http://forum.arcadecontrols.com/index.php?topic=70519.0