Basically, you can always use more than one menu skin object (of same or different type) in your skin, and configure them differently, e. g. to show different parts of the menu.
If you want to use two NAV menus for your portal, then the menu skin object for the root items must have the attributes PopulateNodesFromClient="false" and ExpandDepth="1". The one for the section specific items must have the attributes Level="child", and, to display it vertically, ControlOrientation="vertical".
Other menus may have differing attributes; for SOLPART and TREEVIEW these are described in the Skinning documentation (downloadable from the Downloads section).
Hope that helps!
[EDIT:]
After a bit more of testing, I found out that this solution will not show the Admin/Host items, sorry! For more information see this thread:
http://www.dotnetnuke.com/Community/Forums/tabid/795/forumid/109/threadid/195295/scope/posts/Default.aspx