Well maybe I'm not understanding what you're asking.. What do you mean switching?
When you say 3 sided cocktail I assume you mean controls on either end of the monitor vertically and a set of sticks along a horizontal edge.
Vertical games are normally presented 'rotated' 90 degrees on a horizontal monitor. If you'll be sitting at the monitor vertically for those games you just tell mame not to rotate it by turning off the rotation feature. This is automatic depending on if the game is classified as vertical or not. If you were sitting where the monitor is horizontal to you, the games would look sideways. But since you'll be moving to the end of the cabinet to play the games vertically they'll be correct.