You can do this with one or two sitemaps. If using one, then make sure your sitemap has a strict hierarchy, eg:
<siteMapNode>
<siteMapNode url="Menu1.aspx">
... nodes for menu 1 ...
</siteMapNode>
<siteMapNode url="Menu2.aspx">
... nodes for menu 2 ...
</siteMapNode>
</siteMapNode>
So you keep all of the nodes for the different menus separate, each under a root node of their own. Then at the top of the master page, for menu 1, you have:
<asp:SiteMapDataSource id="menu1Data" runat="server" StartingNodeUrl="Menu1.aspx" ShowStartingNode="false" />
and for the bottom menu you have:
<asp:SiteMapDataSource id="menu2Data" runat="server" StartingNodeUrl="Menu2.aspx" ShowStartingNode="false" />
Now the two menu controls (each bound to a differnt SiteMapDataSource) will only show the nodes starting from their menu. Make sense?
There is also nothing to stop you using multiple site map files, but I'm not sure that's necessary.
Dave