I don't know that you can do this with subfolders and keep the links relative. Basically, best practices are always to put the file in the same folder with PPT -- not in a subfolder -- and then insert the file / link to it.
If you use Package for CD (and opt not to include the PPT Viewer), it will resolve all the linked files and include them in one (packaged) folder along with the PPT file. I know that's not what you're asking for, but it's the one reliable way I know to make your links relative.
FixLinks Pro might help, not sure. It's available at
http://www.pptools.com Just some thoughts....