iWeb will not let you do anything HTML related. You would have to export your website to a folder and then go into that HTML and manipulate it. You would then have to put that manipulated folder on your server.
I'm hoping iWeb will get more advanced in Jan. and I'm really hoping that eventually they will make a professional version since they have a professional version of all their other iLife apps now. (iPhoto-Aperture, Garageband-Logic, iMovie-Final Cut Pro etc...)