To include pagination in your theme templates.

<?php
  if ( function_exists('wp_bootstrap_pagination') )
    wp_bootstrap_pagination();
?>

To Include breadcrumbs, there are two different codes bases available.

<?php 
    if(function_exists('bootpresswp_breadcrumbs')) 
    bootpresswp_breadcrumbs(); 
?>

To use the menu in your theme here is the changes to the standard WordPress nav walker

<?php
        wp_nav_menu( array(
            'menu'              => 'main-menu',
            'theme_location'    => 'main-menu',
            'depth'             => 2,
            'container'         => 'div',
            'container_class'   => 'collapse navbar-collapse',
            'container_id'      => 'bs-example-navbar-collapse-1',
            'menu_class'        => 'nav navbar-nav',
            'fallback_cb'       => 'wp_bootstrap_navwalker::fallback',
            'walker'            => new wp_bootstrap_navwalker())
        );
    ?>  

You can see an example in the header.php file on using it in a fully functional navbar