WordPress Create Menu Locations and Assigning Menus Programmatically

Either in your setup file or in your general functions.php, update and include the following code:

// This theme uses wp_nav_menu() in one location.
register_nav_menu( 'primary', __( 'Primary Menu', 'theme-slug' ) );

//get 'your_custom_menu' id to assign it to the primary menu location created
$menu_header = get_term_by('name', 'your_custom_menu', 'nav_menu');
$menu_header_id = $menu_header->term_id;

//if menu not found, create a new one
if($menu_header_id == 0) {
     $menu_header_id = wp_create_nav_menu('your_custom_menu');
}

//Get all locations (including the one we just created above)
$locations = get_theme_mod('nav_menu_locations');

//set the menu to the new location and save into database
$locations['primary'] = $menu_header_id;
set_theme_mod( 'nav_menu_locations', $locations );