I am having a problem with one of the templates I just bought. For some reason, I am only getting 2 masters for the template

Your template itself contains 2 backgrounds, for the first slide and the common slide. Unfortunately, PowerPoint by default supports only 2 slide masters. The third slide in the template is the special printing slide, it is a file named print.jpg in your download. You can use it to create a common slide.

To set it as a background do the following:

1. Open the presentation.
2. Click on the slide with the right mouse button.
3. Choose “Format Background”.
4. Select “Picture” tab, then “File”.
5. Specify picture and click “Apply”.