Arbital comments are very much like Facebook comments. There are top-level comments, and then a single level of replies. You can like comments to encourage the author and highlight good content. Replying to a comment automatically subscribes you to receive updates when someone else leaves a reply; or you can subscribe manually.
If you want to talk about a specific section in text, you can select it and click the "New Comment" button. When you publish that comment, it'll appear to the side of the selected text. Since the pages can be edited, it's possible that your comment will lose its anchor. In that case it will simply become a normal comment and appear below the page.
If your comment is feedback on the text itself, e.g. "Is this misspelled?" or "I think being more explicit here would be better.", rather than a comment about the topic in general, then you should check the "Show comment to editors only" checkbox when creating the comment.
By default, the editor-only comments are visible only to the authors of the page. If you are not an author, but want to see them, you can use the ⋮ menu in the Discussion section.