If you look at the default main HTML template, you see no tables.
The tables that you see are in other parts. They are used to assure maximum browser compatibility for dynamically generated page elements.
Anyway, that should not prevent you from implementing any type of layout for the header and footer of the site pages.
For instance, if you want to lay the navigation bars vertically, you just need to click on the bar marks in the HTML editor to make a menu appear to let you switch the bars layout from horizontal to vertical.
That was explained in this article. Take a look at the "Visual HTML template editor" section of the article.
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