If I understand you correctly, you can do what you want just by using the -rol or -ror tags for command prompt mame when you're running a vertical game. I have a vertical cocktail setup, and the 'player 1' and 'player 2' sides have slightly different controls. (one side has a spinner/joystick and the other side has a trackball/joystick). In addition to this, I have a small 2 player tabletop joystick setup that I can place on the cocktail, which is essentially the 3rd (horizontal position) control panel. Basically, my machine looks like this:
screen
trackball screen spinner
screen
2 joysticks
If I want to play a streetfighter type game, I just run mame as is. The screen is oriented horizontally, and everything is fine.
If I want to play a vertical spinner game like tempest, where player 1 is the spinner side, I run mame with a -rol tag, which rotates the screen orientation to the the left.
If I want to play a vertical trackball game like centipede, where player 1 is on the trackball side, I run mame with a -ror tag, which rotates the screen orientation to the right.
Does this clear things up?
Good luck,
88mph