Hi,
The layout of the Menu is determined by the Direction property set on the SiteMenu tag in layout.Master and by css. The Direction setting really only determines the css class on the div which wraps the menu. If Direction is set to Horizontal then the div will have the css class AspNet-Menu-Horizontal and if set to Vertical it will be AspNet-Menu-Vertical
Whether the Menu actually renders as horizontal or vertical depends on the css.
mojoPortal includes several skins with Horizontal menus and these skins have the appropriate css. See the skins named jwh1, mojoguidetoglalxy, IBuySpy, splitmenu1 and splitmenu2 for examples to compare to your own skin.
I generally avoid using the theme.skin file for setting anything except css classes. If you set specific style properties like fonts and colors and such on the theme it renders inline markup which makes the page heavier. It is much better to stick with css.
If you do want to use theme properties on the menu you will need to add an entry like this:
<portal:mojoMenu runat="server"...
instead of
<asp:Menu runat="server"...
in theme.skin
because the Menu uses the mojoMenu which derives from asp Menu
Hope it helps,
Joe