The theme does have a Page Top widget area and you could add a custom menu widget there. If you have a large featured image on any pages, it will display below that, though. You’d also have to style the custom menu with CSS to make it horizontal, remove the bullets, etc.
I’ve considered styling some widgets in the Page Top and Page Bottom area, but wasn’t sure if most people would benefit from that. Those widget areas are designed to be full-width for adding call-to-action sections.
What would probably look better is if you added a simple menu to the very top of the site. That’s a pretty common layout. You’d still have to style the menu, though. Or you could assign it the same class that the footer menu uses, which is “footer-nav-menu”. You can also add the class “pull-right”. That would probably look pretty good.
There are a couple of ways to do it on the PHP side, but this is the easiest. You can add a call to the custom menu in the header.php file. I’d do it right after the opening <header> tag. That file already has the code for the primary nav menu so you can do something very similar. Like this:
<?php wp_nav_menu(
array( 'menu' => 'tertiary', //name of menu you want
'container_class' => 'tertiary-menu', //<nav> or <div> class
'menu_class' => 'footer-nav-menu pull-right' //<ul> class
) ?>
You might want to consider creating a child theme, though, so your changes are preserved when you upgrade the Flat Bootstrap theme. A sample child theme is provided in the flat-bootstrap-child directory. Copy that directory up to the /themes folder, then copy in the parent theme’s header.php file and edit that.