Articles should be linked from one to another in order, not all to each other, so that the spider is led through your site in an orderly fashion. If you have affiliate links or cross-links between webpages, make them invisible to search engines by using the 'rel = "nofollow"' attribute in your tag. The spider will then not be sidetracked and you will not confuse it. In that way you can lead the spider from page 1 to page 100 logically.
Meta tags no longer have the importance they once had, but it does no harm to use them. Put your keywords in meta tags and add a description that includes your keywords. That may be used by some search engines in the lists. Add a robots.txt file to the top level directory in your server to tell the robots of any directories not to be crawled: check out how to use it on the internet.
You can add a final fourth table at the bottom of the site for links that should appear on every page, such as to your home page, a contact page, and about us page and sometimes a disclaimer. If placed at the bottom the spiders will not see it till it reaches the last page on your site. Work out why this is!
Finally, do not use flash or java navigation unless you want them invisible to spiders. Spiders can not read these and basically that's it as far as search engine optimization goes. There are many other refinements, but if you keep to that structure and use lots of text relevant to the theme you are most of the way there. The SEO mistake most make is to structure their website wrongly and overuse their keywords, and if you avoid that you will be amazed at the difference it can make.