Groovymame will automatically rotate the screen according to your specifications in VMMaker.
Check the "edit settings" tab and you'll see a monitor rotation pictogram displaying how you want you monitor. If you choose "rotate to the right". You'll see two full looking 3:4 CRT screens, with one rotated. Do it this way you get the UI/menu in horizontal but vertical games are rotated to the right and in proper resolution.
EDIT: You must also check the "export settings to mame.ini" box on the 4th tab, otherwise VMMaker doesn't update mame settings for you.