The plugin's website states this:
Q : Can i have more than one theme at once?
Short answer: If you know CSS, yes.
Long answer: Dropdown Menu Themes are class based CSS. So, every menu you add to your site will have same theme. With current configuration you can’t select custom theme for your second menu but you can use CSS to customize your second menu. Every menu created has a unique id.
I'm certainly comfortable with styling things myself, but looking at the source, I don't see where to call the unique ID in the CSS for one menu or another. The only unique classes are those of the menu items themselves (menu-item-48, menu-item-50, etc . . .) and an HTML comment for each div (<!-- Menu Type : navmenu_3 -->)
Has anyone successfully styled two menus differently and can offer some insight?