I've been testing the Cyberduck CLI tool and have found it's still got some bugs. And you're also right that the documentation is pretty weak.
One bug I've noticed is that you have to specify the full path of the file to upload. For some reason the base path seems to be /opt/duck instead of the current working directory.
You also have to provide your access key as the username and your secret key as the password on the command line. I haven't found a way to specify a credentials file, though I suspect that will eventually go into ~/.duck/bookmarks/
So to upload a file called test.txt to a DreamObjects bucket called my-bucket you would do:
duck --username Your_Access_Key --password Your_Secret_Key --upload dreamhost://my-bucket/ ~/test.txt