What is proper file/folder hierarchy in iWeb 08?

I'm not sure if this is an iWeb question or an iDisk question. I had iWeb 06 and created a website, then did the upgrade to iWeb 08. During that upgrade, I think my folders got messed up because here is what I see when I go to my iDisk: Finder/Go/iDisk/My iDisk/Web/Sites/....THEN I see the iWeb folder, but also see a folder called _gallery (which appears to have nothing in it), a file called Sites.rss, my website folder (which has all of the correct folders/files for my created website). If I double click the folder iWeb, I then see a file called index.html and another folder of my website which contains only some files that pertain to one page of my website! I'm sure this has to be wrong, but when I try to copy the correct files from the domain folder, Finder hangs and gets stuck on "preparing to copy" and I have to restart computer. This has happened many times in a row, I just can't seem to copy the files. The website is working now so I'm not sure if I should do anything...?