I have a navigator div that will appear on each page and I was wondering whether I could save it as a seperate file, like I do with js files and css sheets, so I don't have to type everything out on every page
You can save it as document.write statements in a .js file.
If you take this approach you should also create a site map with a plain html link from your home page. Search engines have to have plain html links in order to index your site.
