I haven't used iWeb, however I've seen footnotes handled in several different ways. I would think you could adapt one of these to iWeb, depending on what features it offers:
Do a normal in-text footnote marker that hyperlinks to the bottom of the page. The HTML superscript tag works well for this. Have the footnote hyperlink back to the location in the text, so people can easily jump back to the main text. I have used this method and usually add something like this to the end of the footnote for the return hyperlink: [^]
Same as above, but use a sidebar instead of putting the notes at the bottom. I have a proof of concept site I could send you over PM if you want to see this in action.
Similar to 3, but have a pop-up window appear. This can be more useful if the footnote text tends to be long. Again, lots of examples online.
You can also google "CSS footnotes" to get more ideas.