I have two Y axes, left and right. How can I turn the right-hand axis title, so that it runs up the page rather than down?

Prism (up to version 3) does not let you change the orientation of the Y axis title. But you can work around this limitation. Delete the right-hand title and then use the text tool...

...to create a new title (text object). Finally select that text object and use the "Format...Text" dialog to specify its direction.