Hmmm... I'm not exactly sure about Dreamhost (I use HostGator), but does it have cPanel? Worst case scenario, you can just upload them one-by-one.
With Cyberduck, you need to choose the directory all your sites go under. For HostGator, it is public_html. In public_html, there are folders to all your sites. Choose the right site, and you'll be in the correct directory.