For SEO purposes is it best to place header and navigation code after main content, therefore content part at the top in the code?
That can be done by using css, which is said not to be a blackhat technique, but I would recommend placing your header and navigation first, then your main content. It won't help you out that much more.
ever see a guy with his face coming out of a pants leg or a shoe or somethign? header goes before the content... its why its called a header n00b