Comments are for internal communications with your team members. Comments are not included in exports nor can your payers see them.
1) Navigate to the Payments tab
2) Click on the Payment you'd like to comment on
3) Scroll to the Recent Comments section and click the "Add Comment" button
4) Type your comment and click "Save Comment"
5) Your team members can now view your comment. You can edit or delete the comment by click the the "Edit" or "Delete" links.