There are two ways for a site to be created:
1. Created on nothing at all -- blank. That's the way delivery sites are created. That affords an instructor the opportunity to copy content from another site (generally, the development site for the same course).
2. Created based on the WebCT standard. That's the way most development (not developmental) sites are created. It's the way a site is created when an instructor is going to start from scratch and create all the course materials.
If you already have a version of a course and all you want is to create a similar version, i.e., copy content from another site and then tweak it, then the course site should be created blank so you can copy content from another site.
If you're going to create something brand new, the site should be built on the WebCT standard.