Good so it looks like the driver basically works. No need to restrict it to not create sub-directories.
Regarding the covers, someone with the device is going to have to figure out where the thumbnails are stored so that the driver can be modified to upload the covers. Another alternative is to use the "Share not sync" option when converting MOBI files. (This is likely the same issue as described here: http://manual.calibre-ebook.com/faq....or-android-etc