Definately do a cardboard mock-up as Pointa stated. You'll be kicking yourself if your joystick/button layout ergonmics are all outta wack!! Uncomfortable = NOFUN. And dude, you've got bucklies having a comfortable simultaneous 2-player game on a bartop.... unless the bartop is huge.... which almost negates the reason behind a bartop imo!!
Setting up 2 joys on a bartop is definately do-able though.. you can't go without Robotron or Karate Champ!!!!
Good luck on the project.