I now have many documents (chapters of a book) that contain plain quotation marks. Is there a way to globally change them all to smart quotes in these documents?
Sorry for the delay. I was searching for a way to globally change all quotes in all Documents at once, but was not successful. You can change the quotes in each Document by opening the Document, go to Edit > Substitutions > Show Substitutions, enable Smart Quotes and click "Replace all".
Another try: Do you use Snow Leopard? As far as I know, the Substitions menu does only work on Snow Leopard. It's a bug we'll fix as soon as possible that the menu is shown even if you cannot use it on your system.