Your navigation structure needs to be visible to the search engines. A navigation structure created with JavaScript will not work for the search engines.

1) Add a site map page and link to it from your main navigation. It provides another way for search engines to find out all pages.
2) Whenever possible, provide keywords in text links as part of the navigation structure.
3) Even if your navigation structure is visible to search engines, you may want to have these bottom-of-page links as well. They are convenient for site visitors and provide another chance for the search engines to find your other pages. Another reason of that is basic text navigation.