Actually, I think what you would need to do is replace the <portal:PageMenu in layout.master with this:
<portal:sitemenu id="SiteMenu1" runat="server" useflexmenu="true" hidemenuonsitemap="false"></portal:sitemenu>
and remove it if there is another copy of <portal:SiteMenu
Then in theme.skin
switch the SkinID for <portal:FlexMenu runat="server", change the one that has SkinID="PageMenu" to have SkinID="SiteMenu" and delete the other one from theme.skin that has SiteMenu or it will cause an error having 2 with the same skinid
I tested this and it seemed to work
Hope that helps,
Joe