Hello tier1ip, and welcome to our board.
Using java script menus does not directly affect your SER (search engine ranking)
However search engine bots cannot see the links in a java menu and therefore they will not index your web site.
To overcome this issue just use text links at the bottom of the pages, somewhat like a site map.
If you want to see what your site looks like in text only, as search engine do I suggest that you use:
http://www.delorie.com/web/lynxview.html