Pages determine the structure of your web-site as seen in the admin Content » Pages page. Think of a web-site as a set of pages. These pages are accessed through a menu. You can also link to a page from within another page.
The navigation, or the menu, is a set of links that help the user to navigate through the pages on your web site. These links are automatically created by CMS Made Simple from the page structure. This hierarchy is what drives the menu you see on the left of this page.
Pages can be in several levels, like a tree of generations. The top level in the menu are the parent pages. Each parent page can have children pages, which in turn can be parents to other children.
The page template determines where on a page the navigation is placed.
You can create any kind of navigation you can dream of by customizing a menu template for Menu Manager. However, the default templates should work for most situations as the menu basically is just an unordered list that you style to your liking with CSS. The web is full of good articles about styling a list of links, one of the best is listutorial at maxdesign
Pages in the CMSMS Admin Panel
You add pages, as well as other content (see next chapter), in the CMSMS Admin Panel from the Content » Pages menu.