I don't know the Nanao model no. you refer to, but if it's a 15kHz capable monitor then in mame.ini you can just set the "orientation" line to "rotate_r" or "rotate_l", and, possibly the aspect to 3:4 rather than 4:3. Try first with 4:3 as normal, and if the image is far too tall for the screen, set it to 3:4.
That means you don't need to run VMM again or rotate your desktop.
If you do want to rotate the desktop, do that, and play with the options above to see what rotates and what doesn't. "Horizontal" and "Vertical" are the other orientation options in mame.
VMMaker is amazing, and I'd recommend doing things over because your arcade monitor will have a 16.2kHz scan limit, higher than the 15.75kHz you would have set for your TV. May not make a huge difference, but I use that capability. I have a serious problem with VMM's option for a rotating desktop though - things just never seem to go smoothly. It's probably that I haven't spent enough time learning it

Your frontend is up to you
