How to update a Web Site

Rename your Web.Config to Web.Config.Old
Copy the current files into your staging site folder, overwriting all
Copy Database and license information to new Web.Config
Copy in Custom pages
Compare the ChangeLog.aspx page of the old site (which should normally be in Source Control) to the ChangeLog.aspx of the new site and make any required changes to Custom pages.
Test Site as needed
Publish Staging to Live