Take your mouse or trackpad and select a piece of text (highlight it). You will see a small annotation bubble come up. Make your comment and save it. Your comment will display in the margin to the right of the text. Click on the comment bubble to edit it or delete it (use the edit and delete icons in the upper right corner of the comment bubble).
If you are using an iPad (or other touch device), select text by touching the screen. Then you will see an Annotate button in the lower right corner. Click it to write in your comments and save. The rest is the same.