Danny, you only need to upload/install the theme via plugin manager, then go into your course , click Theme Picker on the left menu and you will see the themes you have installed. click the theme and save to use it for the course. You select a theme for each course you create. but like John said, in the AT you still can only use one theme at a time for a course. To switch a theme just go back to the course menu page and repeat the steps