I have been play around a lot, trying to upload a whole folder ( without compress it) to the cloud service but no luck.
The official position from Adobe at the moment:
"Currently you cannot upload folders, just individual files.
When Creative Cloud Connection is released within a few weeks you will be able to sync files and folders from the Desktop to the Cloud.
The only workaround for now is to create a folder in the Cloud. Then you can upload multiple files to it at once via the upload button or using drag and drop. The only browser multiple file upload will not work in is Internet Explorer since Microsoft explicity designed their browser to not allow multiple file upload."