Anything that isn't the PHP or JavaScript ad codes are violations of the TOS. And doesn't iWeb generate standard .html pages? Just manually insert the JavaScript ad.
Yep, in cPanel, click File Manager, click the www folder icon, find your file (whatevername.html), click Edit File, and put all the ad code just before the end of the </body> tag (If you're on advanced), or just after the <body> tag?