"I'm not sure how/where to store HTML referenced materials in ZC. I have .jpg, .png, .swf and .xml files that all need referenced by either HTML code in ZC or by the .swf files."
Product-related images would reasonably go in the base /images/ folder, where you would address them by
<img src="images/yourimage.gif" alt="Your Image" />
I'm not sure of the best place for .xml files; .js files have a special folder setup, described in detail in the wiki article on using javascript.
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