Hello,
Jay says correctly that you could ensure this behavior by API. The basic method is:
PageTemplateInfoProvider.AddPageTemplateToSite(pageTemplateId, siteId);
See the API Reference here:
http://devnet.kentico.com/downloads/kenticocms_api.zipRegards the empty folders: we will change this behavior in the next (5.5) version. Now, it works in this way because of performance, however, we will improve it in the next version.
Best regards,
Helena Grulichova