Unfortunately it is not possible to change the location of the websites folder. The installer always searches for it in the main folder where Sitefinity is installed.
If you want to create a project in another directory, you have to do it manually. Just copy the content of the /Projectmanager/EmptyProject
folder to the new location, set the necessary permissions (make sure you allow full control for the ASPNET account), and then create a new virtual directory in IIS pointing to your new folder. This project will not appear in the project manager, though. To list it there, simply add a record for it in /ProjectManager/App_Data/Projects.xml.
the Telerik team