I think that the problem you are experiencing may be due to the way you are crafting the template to include as your SiteAssist layout. Instead of adding in the menu to the template you should just save the page as a template and create a new SiteAssist layout based on this template minus the menu. You can also use the CSS Sculptor preset directly without making a template from it first, you just select the CSS Sculptor preset that you created. There is more info on creating the SiteAssist Pro layouts with CSS Sculptor and Menu Writer in this document that can be found on the SiteAssist Pro page under the FAQ:
Also, for the screens that seem the same the first set is for the home page and the next set is for the content pages in case you would like them to look different. If not you would do the same steps for both sets of pages.