I'm not sure why you would want to use iFrames for those regions, i would suggest just creating Template regions and place the menu and footer in those regions. This way Dreamweaver will render the design correctly.
So once you have your sculptor page, create the different regions (header, menu, content and footer) and create the template and then apply CSS Menu writer to the template directly. And if you are going to use SiteAssist Pro, you could use SiteAssist Pro as your starting point, because SiteAssist Pro will create the Template and different regions you needs (header, content and footer) and you could more regions if you wanted. And the menu that is created from SiteAssist Pro you could customize with CSS Menu Writer.
In regard to the WebAssist login, that is a security feature and I'm not sure if there is a way around it.