Derek, I think you're trying to create a new directory in the root of the primary site. This is not allowed. All your sub directories go with html or files and can be referenced from there. For example, I've created a directory under the html directory called "images". In my HTML code, to reference that directory I put:
src="images/brummnet.jpg"
Basically Apache see's the doc root as being "html" and you can reference your subdirectories from there.
Hope this answers your question.
Terry