You can create Web.config transform files for publish profiles as well as for build configurations. When you publish, either in Visual Studio or from the command line, Visual Studio applies both the appropriate build configuration transform and the publish profile transform. See this tutorial:
This is one of a series of tutorials. Others in the series run through examples of creating publish profile transforms and examples of doing it from the command line.
The tutorials use a web application project. If by web site deployment you mean you're deploying a web site project, the process is basically the same as long as you have installed the latest VS update (see the first tutorial in the series for links to the VS update).