When it comes to the folders and the files that reside in them you do not need to create the structure if the pages already exist and links are going to them correctly. Only if the pages need to be in these directories and the directories are not there would you need to create them manually.
As for the problems you are having with the template you could check on the pages that are derived from the template. At the top of these pages should be a reference to the template file. If the reference is in place then any updates to the non editable regions of the template should propagate to all the pages derived from it.
The template functionality is not a property of SiteAssist but is built in Dreamweaver functionality, so long as the pages have the reference on them the updates should work for all the pages. If not there may be a problem with your current DW instance. If this were the case restarting DW and recreating the site cache should help to clear things up.