Hi pajackson60, you can try pasting the code into the wordpress post to see if the image map keeps working well after being processed by the WP internals, but it depends on the links inside your code if the FancyBox gets appended automatically.
Are you linking to images or PDFs or Flash files or Youtube pages from within that map, and did you not disable the image link auto detection under the FancyBox settings, then yes, FancyBox should kick in automatically.
Otherwise, no. You'll have to append the appropriate class names manually. And which class depends on the target. For example, if you are linking to another web page, use class="fancybox-iframe".