You should be creating your new SiteAssist Pro layout first before trying to use the SiteAssist Pro wizard. When you create a new layout you should be able to choose your template or css sculptor preset and the menu you would like to have in the site. Once you have completed the process you can then go into the SiteAssist Pro wizard and generate a site with the new layout.
SiteAssist is designed to generate a static site, it does not create a dynamic site that utilizes includes for the content.