I don't think this can be done, as the browser determines how it will render an IFRAME, and this is typically treated as a "hole" in the page showing the framed page "underneath". Since our overlay-style cart is dynamically rendered as a part of the same page containing the cart button code, an IFRAME "hole" in that page would punch a hole through the cart as well.
If you can't eliminate the IFRAMEs, about the only alternative we could suggest would be to use our non-Javascript cart button codes which open a separate window/tab to display the cart instead of rendering the overlay into your page.