Menu structure

Hi,

What is the best menu structure? I tried creating one category hidden menu item but it did not work. I also tried crating a single item hidden menu bit it did not work.

1. Do I need to create a hidden menu for each category? Do I have to do it for subcategories as well?

2. What happens when more than one category is assigned to an article? Which menu will it route through? Will this create duplicate content and result in google search engine penalty?

If I leave it on the homepage and do not create category menus, it gets routed through the homepage and I do have some extra information on homepage that I do not want displayed when reading an article.

Thanks