In previous editions of Office, you could just put the PowerPoint template in your templates folder. However, this is not the case for 2013 after I spent some time trying to work out why they were not appearing. With the help of this blog, I got the answer.
PowerPoint 2013 allows you to define what directory to use for your Templates folder in the Options under Save. See the screenshot below.
Once in PowerPoint and you go to File > New, you can now see you have an option for Personal and then your templates are available to choose from. This is the same for Word and Excel.
Hope that helps some people.