you don't have to use Cyberduck if you don't want to.
As you know you can use HTML Snippets to add HTML codes. However they don't work for all codes. There are codes which don't work in HTML Snippets. And add these codes you have to use what I call Alternative HTML. If you use that you can't use the iWeb integarted FTP. Hence have to use an FTP application and Cyberduck is the best.
Also if you want to add a menu like drop down or tear down or accordion menu to many pages you would have to add an HTML Snippet with the code. If you then would like to update the menu perhaps adding a new page you would have to change the code in the Snippet of every single page. If you have 300 pages like me it's an awful work. With alternative HTML you change it once for all. Again you can't use the integrated FTP afterwards.
The iWeb integrated FTP can't be used to upload files which are not part of iWeb. Example: Flash videos, Flash players, source files needed for a menu, a photos slidesho. And more.
Bottom line there are many situations where you HAVE to use an FTP application (Cyberduck or other).
Of course if you don't use anything and only use what iWeb provides (which per se is really not much) you can use the integrated FTP as well.
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