I suggest stepping away from the whole DreamWeaver "get" / "put" model for a moment, so you can get a decent look at the state of your directories.
I suggest using a real FTP/SFTP client, or ssh in the shell, so you see the "whole picture" and can visually confirm what you "current" (result of all your experimenting) directory tree really looks like. From there, it should be pretty easy using those tools to "re-structure" your tree as desired/needed.
It's really hard for me to be more specific as I can't see your user space and it seems you may have "confuzzeled" things considerably while doinking about with it all.
Well, it shouldn't matter if you are connecting directly to the server instead of via "hostname", but if "hostname" is not properly pointing to your dreamhost space ("parked elsewhere") it will make a huge difference - using that hostname is DreamWeaver you will be working in/on that data structure if you can even log in (which you probably can't!).
Plus, if that domain is "parked" somewhere else", how are you even borwsing to your DreamHost user space in order to see the "Index of" stuff. That, with no files listed, simply indicates that your site files are uploaded to the wrong directory.
Seriously, at this point, abandon trying to "fix" it via DreamWeaver until you know what the existing structure actually is, and have put it in order so that the directory indicated in the DH control panel for that domain is actually holding the domain's files.