EDIT: I did not read properly the last bit of your post. If your files are not
in the same file directory structure, well at the very least you need to know
exactly where they are in the actual file structure on the online website,
otherwise how are you going to include them in the mirror, which is a Copy of
your website?
You will have to manually create folders (or maybe have WinHTTrack create them
for you during a mirroring operation) and manually put the files in the right
folder structure. I'm not sure what else could work.