Menu Confusion??

I am a newbie to WordPress and I am very used to Joomla and maybe that is my problem. Here is what I am having trouble with. I have a template that places the main nav menus at the top. I have created 15 pages. They all show up on the top menu and I do not want all of them to show. I can exclude them with a little plugin but then the left widget that I have for some of the pages do not show up as well. What I am trying to do is have some pages show on the top and the other as a page widget. I can setup the widget fine but when I use the plugin to exclude certain pages from showing on the main nav they also don’t show on the widget. How should I be setting this up???

HELP!!