What does 'Apply Template' do?
This copies the settings of another project to the current project, except for the images and the control points. This function is accessible both from the 'Apply Template' item in the File menu, and from the toolbar in PTGui. A template can be any PTGui project. In Tools/Options/Folders&Files, a folder can be configured where you store your templates (on Mac go to the PTGui menu, Preferences, Folders&Files). Then, the template selection dialog will by default open in this folder. There's a little triangle button next to the 'Apply Template' button on the toolbar, which shows a drop down list of all templates in the configured template directory, for quick access.
Templates can be useful for a quick initialization of a project (lens settings, rough alignment of images), although this is usually not necessary anymore, now that the Project Assistant in PTGui 5.0 and later automatically initializes the project.
Another use for templates is when you have an exact reproducable setup (high quality panoramic head with fixed angles). In this case you could copy all settings of a previous project and there would be no need for placing control points and optimizing.
http://www.ptgui.com/support.html#2_14