Problem Uploading with CyberDuck to GoDaddy host site

I created an iWeb site that looks and functions fine on my computer (10.5.8). I successfully uploaded it with Cyberduck (3.2.1) to be hosted by GoDaddy on a domain I own. At that point, everything was lovely. Then, I revised the site in iWeb on my computer. When I uploaded it to GoDaddy with Cyberduck (overwriting the previous version of the site), most of the online pages had lost some formatting and many of the links no longer worked properly. At that point, the revised iWeb site on my computer still looked and functioned fine. GoDaddy help did some troubleshooting and concluded that the problem is with iWeb or Cyberduck.
I'm stuck. Any ideas?

Tom,
Please click on "The Concept" button to notice margins and spacing on that page. On most pages, the "Order" and "Contact" buttons in the box at the bottom of the page don't work. The titles in the "Archives" section don't link to the articles as they did in the iWeb version on my computer. What can I do to avoid these errors in future uploads?
Also, is there something I can do differently to make the brief "Welcome" QuickTime video (on the home page) work on IE?
I expect to add/change the site every couple of weeks. Is there a way to upload just the changes and not overwrite the whole site?
I value your help very much. Thank you for taking the time.

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