So I think I have come closer to understanding my issue..
Since there are multiple files and a linked XML file, there is some disconnect since I can't have all of the files together. I think this is why part of my flash movie shows up but the controls are messed up and the pictures are missing.

Example.. I think all of the files (.swf, .xml, images folder, etc..) want to stay together. However, the mainpage is loading from includes/templates/mytemplate/common/ and the flash files are from includes/templates/mytemplate/FLASH/

I'm not sure how to get this to work.
Anyone have any experience with this sort of thing?