Go to your admin panel > design > menu
Here you can create your own, personal menu. Add your homepage and other pages/categories to the menu. Afterwards you can order them by drag'n'drop the elements (in the menu editor on the right).
The shortcode for columns must be added to the text in the wordpress editor - so where you write your posts and pages.
You get 3 columns by adding this in your editor:
[one_third last]Content here.[/one_third]
[one_half last]Content here.[/one_half]
Everything is also described in the template documentation.