Header (site header) is the standard area where you would normally find the logo, site title, site description as well as any header widgets.The Navigation can be positioned below this in the Layout > Navigation > Navigation location below header.
PageHeaders are an awesome add-on for GeneratePress and they replace the featured image on a page or post. And as standard they sit below header and navigation.
PageHeaders can be merged with the site Header, so you can have the image behind the navigation and site header.
If you intend to use PageHeaders across your site then i can walk you through that and give you a little CSS code to move the navigation to the bottom of the PageHeader?