With the new version of SiteAssist Pro you can create your own layouts based on a DW template or a CSS Sculptor preset. You would do your editing to one of these, then incorporate that into your new layout for SiteAssist Pro. You could then update the existing site and just use your new layout.
In addition to the design of the site you can also include your own menu in the layout. This relies on using a preset from CSS Menu Writer. You would craft the look and feel of your menu in here, then use the preset for your new SiteAssist Pro layout.
There is a bit more info on this in the support page for SiteAssist Pro, here is a link:
Check out the customizing your layout with CSS Sculptor and CSS Menu Writer.