It is generally recommended to keep as flat a structure as possible when planning your web site presence. That does not mean however you need to throw everything in the root directory for best results. You should not go more than 2-3 levels deep in your directory structure.
Each major theme or category should become a subdirectory within the root. This is a simple, easy, efficient way to organize your site.
To increase visibility, each layer must act like an independent Web site
Site maps are a great way to be sure all of your pages are indexed.
A link to a site map page on all of your pages is a great idea.
They make it easy for the crawler to crawl the whole site
Make sure the site map is available to your users, not just the crawlers. This will increase usability, and give your users a list of links that point to the important parts of your site.
If the site map is larger than 100 or so links, you may want to break the site map into separate pages.
Short link paths are better – users should be able to access sub-pages by traversing a minimal number of pages from the start page. The deeper the page, the more specific the content should be, and the less importance search engines will give it.
Don’t use pop-ups. These are penalized heavily by Google.
Use header tags (h1, h2, h3) for content hierarchy: h1 tags for the page topic (ie. use only one per page), h2 tags for a topical headings, and h3 tags for sub-topical headings.
It is recommended that you have an identical navigation menu on each page, with navigation links based on keywords.