> Question do I copy all downloaded files to cd and
> then point to the main home page? Should I alter
> anything? Do I just download whole site as normal?
For best compatibility with CDs, you should mirror a website with the option
"Build > ISO9660 names" ticked.  You may also want "Build > No external pages"
ticked.

Then copy them to the CD along with your autoplay program pointed to the
homepage (index.html) or whatever.