After enabling internal comments for your post types of choice on the plugin’s settings page, you can find the internal comments meta box on the edit screen of applicable posts. The meta box is titled Internal Comments and is where existing comments can be viewed and/or edited, and also where new ones can be posted.
Posting new comments
To post a new internal comment, go to the page/media/post you want to comment on and type in the text of your comment inside the New internal comment text area. Lastly, click on the button Post comment.
Posting new private comments
Private comments are available only if they have been enabled on the plugin’s settings page as described here. If available, a private comment can be posted by simply checking the Mark as private checkbox before clicking the Post comment button.
Private comments are only visible to the original author and other users that have the proper capability. Read more about the internal comments permissions list here.
Replying to existing comments
To post a reply to an internal comment, navigate to the bottom right corner of the comment and click the Post reply link. A new text area will appear where the reply can be written. Afterwards, click the button Post reply to finalize your action.
Replies to private comments are always private as well. It is not possible to create a non-private reply to a private internal comment.
Editing existing comments
To edit an existing internal comment, simply navigate to the comment in question and click the Edit comment link. A new text area, prepopulated with the current comment text, will appear. After editing the text, click the button Save comment to finalize your action.
Previous versions of the comment are available while reviewing the revisions history. Learn more about it here.
Deleting existing comments
Deleting an internal comment is as simple as navigating to the comment in question and click the Move to Trash action. If the WordPress constant EMPTY_TRASH_DAYS is set to 0, the action will be named Delete since there is no trash anymore.
Not everyone can edit or delete comments (not even their own). By default, only administrators have the required permissions. Read more about the list of custom permissions used by the internal comments plugin here.