Facebook comments plugin is included in the recommended plugins list. After installing Boombox theme you’ll find that plugin under the plugins list, which system recommend to install. After installing and activating that plugin, you can find options related to it in Customizing ▸ Single Post ▸ Main under Sections position.
Facebook Instant Articles support is integrated via official Instant Articles for WP plugin (built by Automattic), available for free download in the WordPress.org repository. You can also install it directly from the WP admin ▸ Plugins ▸ Add new. After installing the plugin configure Facebook Instant Articles in WP admin ▸ Instant Articles.