How do I make a new-project's folders, which are created from a custom project template, point to the newly created directories?

I'm using LabVIEW 2013 and developing a custom template witch will create a new project that contains auto-populating folders.  When the new project is created the directories are replicated to the new location as desired, however the links in the lvproj tree still point back to the location of the source of the template.  I want these to be a relative path to the project and not an absolute path.