Without having a site link we can test and look at directly, we can only give general advice here which may not address your actual issue. It's okay, people post links to unfinished sites for us to look at all the time; if you wish, you can send it to us privately via email:
That said, first of all you do need to have your store pages published/uploaded to a live Web server for the cart to work; the buttons and cart will not work properly on a "local" copy of a page that's only saved to your own computer's hard disk alone and not accessible online.
iWeb also has a known issue where any HTML code-snippet widgets (such as our button codes) that you insert into an iWeb page do not actually get inserted directly into the raw source code of the page itself. Instead, iWeb saves each snippet you insert as a separate file, and it puts <iframe> tags in the main page that point to that separate snippet file. Our cart button codes (especially the View Cart button that makes the nice cart overlay work) cannot work properly with this iframe method, as our codes must be pasted directly into the raw HTML source of the page itself.
If iWeb does not allow you to edit the raw HTML code of the page directly somehow, then here's a trick you can use. Instead of pasting our button codes into iWeb, just use iWeb to perform all the "heavy lifting" of overall page layout and design, and type some placeholder text like XXXXX wherever and however you would want our buttons to appear on the page, then save your pages/site and close iWeb. Then open those same Web page files using a plaintext editor like TextWrangler (a free, very good app for this task), find the XXXXX placeholder text in the code, and replace that with our button code.