What are the steps that you are taking to create you new site design in Site Sculptor? You should start in the preset manager and create a new Site Sculptor Site Design. When you do this you should be able to select a CSS Sculptor preset or a template for the home and content pages. The templates should not have a Menu Writer menu on them, this is configured in the next step. Once you specify the template and the menu and areas for the home page you can do the same thing for the content page.
Please post back and detail the steps that you are taking and include the templates or presets that you are using for this.