Fixed - Thanks Ray!
Here is the answer in case anyone comes across this with the same issue. Most likely this is old news and I was the only one that had the issue.
It's as simple as making sure your paths are site relative rather than just page relative so that they can be read from any directory properly. For example on my index page an image link with a correct path of: images/thisimage.jpg which works fine in the site, is broken in the admin_cms directory. Adding a "/" in front makes it accessible from anywhere: /images/thisimage.jpg
I know, duh!
The answer to my second question regarding the difference in the code in developer notes and what is produced in dreamweaver is the include in developer notes is already covered in the "require_once" code at the beginning of the page. Makes sense now.
