ok, I did some testing with Nvu, and I believe I may have fingured out the issue.
Nvu can't create subdirectories. It can only publishing to existing directories. When you try and publish the page you have created to a directory that doesn't exists, such as ftp://www.domain.com/domain.com/new_directory/ Nvu returns with an "Unknown Publishing error".
It also seems that if you "Edit Sites" and change the settings as to where to publish, you will have to exit the program and launch it again to get the new settings to take effect. Nvu apparently is sure that you want to keep publishing to the same place, even if it didn't work, during a session.
So, the problem isn't with your settings, it's with the short comings of the progrm. Nvu is a nice WYSIWYG, but as a ftp client it has some serious issues. What I would sigguest is that you download an FTP client to publish your files. Read this K-base Article for some basics about FTP and some sigguested programs. If you're running windows XP, be sure and read the top most user comment on that page.
The way this will work is that you use Nvu to create all of your files, and you save them on your computer. Then you open up your FTP client and use it to publish your site. You could of course use the Ftp program to only for creating your directories and then use Nvu to publish them - but that seems like more hassle to me.
As far as the seconed error that you posted about, I'm not sure where you're getting this 'userid'. I would sigguest that you click "edit sites" on the left hand side of your screen. Select the site, then fill in the fields. Make sure that the publishing url is ftp://www.mydomain.com/mydomain.com/ Then close that box, save any open files, exit the program, relaunch, and then try again. (note, however, that the example url will publish to your main site area - you'd go to www.domain.com to see the files in a browser and it still won't create that sub-directory for you )