When you create or modify a site with SiteAssist pro it will insert the default menu for that layout. The way to get around this is to create your own layout and incorporate your CSS Menu Writer menu directly into the layout. That way when you alter the site through the wizard your custom designed menu will still be there.
To create a new layout just use the Layout or Preset manager depending on what version you have installed and just go to new layout. It will prompt you for the menu preset and the Sculptor preset or a template file. On the SiteAssist support page there is a bit more info about creating custom layouts.