Q) how to design a site with SharePoint designer that later on has to be converted to be a SharePoint site
A) Sharpoint sites uses Master pages, CSS and JS.You can develop your website by either using existing Master Pages from WSS / MOSS and start branding it, or start with minimal Master Pages to start with.Minimal master's gives you more freedom and you can start producing sites based on your design layout and theme.
Check these links
How to: Create a Minimal Master Page http://msdn.microsoft.com/en-us/library/aa660698.aspx
Building Simple Master Pages for Windows SharePoint Services 3.0
Modify the default master page http://office.microsoft.com/en-us/sharepointdesigner/HA101009061033.aspx
Best place to start is heathersolomon's Blog Posts, She discuss indetail about sharepoint customization and check Minimal or Base Master Pages http://www.heathersolomon.com/blog/articles/BaseMasterPages.aspx
Best practice for Style Sheets are not to modify Core.css and use your own CSS file and attached that to your site.
Apply a custom style sheet to a SharePoint site http://office.microsoft.com/en-us/sharepointdesigner/HA101691741033.aspx
Customizing SharePoint Themes with SharePoint Designer 2007 and IE8 http://blogs.msdn.com/kaevans/archive/2009/03/08/customizing-sharepoint-themes-with-sharepoint-designer-2007-and-ie8.aspx
Demos: A six-part series on getting the most out of SharePoint Designer 2007 http://office.microsoft.com/en-us/sharepointdesigner/HA102199841033.aspx
You can use navigation menus available with WSS / MOSS or you can write your own Navigation menus for your site.
MOSS Navigation Deep Dive series http://blogs.msdn.com/ecm/archive/2007/02/10/moss-navigation-deep-dive-part-1.aspx
How to create custom navigation menu in SharePoint with XML data sourcehttp://blogs.msdn.com/matjazperpar/archive/2008/12/17/how-to-create-custom-navigation-menu-in-sharepoint-with-xml-data-source.aspxand importantly
How to Optimize a SharePoint Server 2007 Web Content Management Site for Performance http://msdn.microsoft.com/en-us/library/bb727371.aspx
Also check MSDN SharePoint Team Blogs