In the layout.ascx (layout.master in mojoportal 2.x) file there are attributes on SiteMenu such as SubMenuCSS that are passed through to the skmMenu.
I'm assuming you are using the 1.x version of mojoportal. It is possible to use skmMenu in 2.x mojoportal but the preferred menu is the ASP.NET menu.
SiteMenu control is a wrapper around skmMenu in mojoportal 1.x and the attributes are passed through to skmMenu.
In mojoportal 2.x SiteMenu is a wrapper around skmMenu, ASP.NET Menu and ASP.NET TreeView. however the attributes on SiteMenu only apply to skmMenu.
In mojoportal 2.0.x the ASP.NET Menu or TreeView is styled using the theme.skin file, but in the not yet released 2.1 branch we are using the new CSS contol adapters for Menu and TreeView and these are styled using CSS in style.css
Hope it helps,