I had the same problem.  I resolved it by specifying the following attributes for the main menu CSS classes in skin.xml:

rootmenuitemcssclass

rootmenuitemselectedcssclass

rootmenuitemactivecssclass

menuitemactivecssclass

Then in the skin.css, I added my classes defined above and rewrote the following CSS classes for the submen:

.MainMenu_MenuItem

.MainMenu_MenuItemSel

These submenu classes must come before the root menu classes defined above.  Let me know if you need further clarification, but I was able to change font color/size/etc of the submenu using this technique.

The order matters because this is how CSS works, pickup a book about CSS or check out an online tutorial

You add an attriubute to the nav skin object, e.g. CSSNodeRoot="myrootmenuclass", and than: .myrootmenuclass{color:green;}

Peter