Is this something like the horizontal nav is for the main, top level links, and the vert nav is for the sub pages?
If so, check out the blackcandy theme that comes included. It is setup like this already. Dig through the templates to see how its down.
Or you mean you have 2 navs for different pages and they never show up at the same time? You'd have to setup different page types for each by extending the Page class and associate the template with just the code. Or run a bunch of <% if inSection(page) %> checks in your template to see which page you're on and display the correct nav.