Use mala as your front end-it has all the vertical options you'll need. I have a vert cocktail machine and what happens is that windows will come up horizontally, but mala is rotated for the correct orientation when it loads. (there are settings in mala for rotating it)
With the arcadeVGA you should use the auto resolution tool to create .ini files for every game.
When you launch the game from mala, you may have to use the tab->video options->rotate view to get the game into the right orientation. You'll have to do that for each game, but only one time per game. (that's part of the fun of MAME anyway-trying them ALL out!)
-jeff!