When you edit the css for the menu on the home page you should edit the css directly if you are having trouble getting your updates to save. The menu file is in CSSMenuWriter > cssmw_home > menu.css. There is also the menu_ie.css file. It is in here that you want to adjust the css. The setting you specified is the correct setting for the sub menu items.
You will not be able to edit the menus within the SiteAssist wizard. Instead you can use CSS Menu Writer to create or customize a menu, then incorporate that menu into a custom layout for SiteAssist. We have some guides that cover this on the SiteAssist support page under How Tos and Solution Recipes.
When it comes to modifying the home page you will not be able to change the page type in the wizard. You can specify the home page when creating a new layout though. If you want to add to the existing page you should do so directly on the page.