I can better comment on specifics if we decide on a visual solution first. Since comments can be added to almost any mapping element -[Obj|Db] [Entity|Attribute|Relationship] Query (?), my first thought is to add an info button (same as the one used on relationships panels) to the rest of the mapping elements. This button would pop a dialog showing comments editor.
If comments are hidden behind a button, than the button should have at least 2 different visual states, to know from the first sight if there's a comment there or not (without the necessity to press the button, open a window and than find out that there's no comment there).
IMHO much better approach would be to have a "comment" field with an [..] button like one is used in all GUI designers. Clicking the [..] button opens the popup to edit. In the same time one can see if there's something in that textfield or not. Ahmed.