It might be helpful to back up slightly too, since you seem to be confused about how the menu itself gets on the page. If you take a look at a layout.master file for a delivered skin, you will see the site's menu gets included via a portal element like this (from the layout.master of the andreasviklund-02 skin):

    <div id="topmenu">
    <portal:SiteMenu id="SiteMenu1" runat="server"
                UseTreeView="false"  HideMenuOnSiteMap="false"
                Direction="Horizontal" TopLevelOnly="true"></portal:SiteMenu>
    </div>
 

That places the menu in the same spot on each page (in this case, TopLevelOnly is used since a vertical menu will also be used on pages as needed for the second and lower options). Again, from the andreasviklund-02 skin, this is the code for the left content pane, with the vertical menu declared:

        <asp:Panel id="divLeft" runat="server" cssclass="leftside" visible="True" SkinID="pnlPlain">
            <portal:PageMenu id="PageMenu1" runat="server" UseTreeView="true" TreeViewShowExpandCollapse="true"  />
            <a id="startcontent"></a>
            <asp:contentplaceholder ID="leftContent" runat="server"></asp:contentplaceholder>
        </asp:Panel>

Once the menu(s) are placed in layout.master,  then as Joe said, you style the elements of the menu using CSS. You may want to review this document to gain a better understanding of how the mojoPortal layout.master file works, and how all the elements of the page are placed.

You really don't want to "take control" of a menu by putting it into an HTML element. The power of a CMS like mojoPortal is that the site builds your menu dynamically for you. You just tell your skin where it should be placed, sit back, and watch the magic happen.

Jamie