I am creating my first mojo portal site.  It has been quite an experience, but I am sure I will get much faster with everyone I do. 

I have mojoportal configured for multiple sites.  the site I am working on right now is to be the 3rd site.  I have the skin working and the pages created, however, I do not see them on the menu.  I changed the toplevelonly setting to false in the layout.master and still I only see the Home page link.  I have even moved the pages around in the hierarchy.  Can anyone tell me the best practices for setting up these sites?  Should the Home page of each site be on the root level and other pages for the site under it?  I have watched the site hierarchy videos and I understand how to move the pages about, I am just now sure how to set this up when multiple sites are included.

Thanks!