As John Saunders said, avoid web site projects like the plague. You can turn your site in to an application by right clicking on the site and selecting "convert to web application" but be warned that you will need to do some rework on the project structure and code.
If this isn't an option then you can add them to TFS by right clicking on the solution in solution explorer and select "Add Solution to Source Control"
This will add the solution and any projects contained within to TFS, including the web site. It will create the TFS bindings in the .sln file