Edit Navigation in Magazine theme

I would like to do 4 things in regards to the navigation bar in the Magazine theme:

1. Control what pages are shown on the navigation bar.

2. Control what categories are shown on the navigation bar.

3. Control whether a category or page is nested into a menu or not.

4. Control the display order of each item on the navigation bar.

If there's a way to use the built in wordpress menus I missed it so please let me know.