I think that you should start out with CSS Sculptor to get your layout setup the way that you want it. Once you have created the layout in Sculptor you may want to craft a custom menu within CSS Menu Writer.
With that part done you should use your new Sculptor preset to create a new SiteAssist Pro layout. When you are crafting this you can choose one layout with a menu for the home page and another for the content pages, so having the horizontal menu on the home page and a vertical one on the other pages will work just fine.
When you do all that you can then run SiteAssist Pro to generate the site, this will create the template for you.