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):
<portal:SiteMenu id="SiteMenu1" runat="server"
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" />
<asp:contentplaceholder ID="leftContent" runat="server"></asp:contentplaceholder>
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.