Absolutely. That is one way to do it. The other is to create the template with the navigation and background and then import the pages into it. Either way, you have work to do lining things up.
If you are using PowerPoint to storyboard, one way to do this is to create your template first and then take a screen shot and use it as the background in the PPT. That way, things will more likely to be close to the right place.
