A help project template is simply an entire Help+Manual project with all its settings, including all your styles and all the settings and items in the Project Explorer. A project template can include topics with content but it does not have to. If you have topics that you always use (for example terms and conditions, introductions and so on) you may want to include them.
Unlike HTML skins, project templates are used as a model for new projects. You can also apply project templates to existing projects but this is a little more complicated (see below).
Skins are applied when you publish and do not affect the settings in your current project, the settings in project templates become an integral part of your project.