The core concept is that there are potentially two panes: the main text pane, and a lower comment pane below. (Yes, this idea is lifted from Word.) They are contextually linked -- insofar as possible, the panes try to stay in synch with each other.
To create a top-level comment, you highlight a bit of text in the main window; this activates the "comment" button. If you press that, the Edit Comment pane/window pops up (this might be either a popup window or the bottom pane). It lets you enter a new object, which descends directly from the Comment type -- in theory, this type should be as configurable as everything else. Once entered, the comment adheres to the main entry, and specifically to the highlighted text (which means that it's editing the text to show the borders?). In the usual rendering, it shows up as a slight highlight to the chosen text (maybe a cream-colored background, or somesuch).