How to edit presenter notes in Keynote '09?
Unfortunately, Keynote '09 can't achieve such a feature. You can, however, this feature has been added in the 2013 version of Keynote.

Enable the presenter view (in this example, I'm going to use the "Rehearse Slideshow" feature).

If you don't see the presenter notes, go to the top right corner of the screen and select the middle icon, then check off the "Presenter Notes" box.

Now that you see the presenter notes, it may not look like you can edit them at first, but if you slide your cursor to the top right corner of the notes box, the "Edit" button will appear. Click on it, and start typing (you can also edit it by double-clicking anywhere on the box).

Hope this helps.

(P.S.: For some reason, I'm unable to upload any pictures in order for me to show you better. Once StackExchange fixes those bugs, I'll update the answer with the appropriate pictures).