It just so happens i had this same problem inputting the full page script into my SMF 2.0 RC3 boards , whenever i did add it into my index.php or my index.template.php it would either A. stop my preview post option and B. stop my shoutbox from auto updating , or It would change the sizes of all sort's of my controls...........
I am however going to tell you the seamless easy way of doing this.
Goto your admin panel in SMF , Install this mod:
http://www.simpleportal.net make a bottom block in your new settings , put the full page adf.ly script into a block of custom html coding , and it will work without interfering with anything else

Problem Solved......
you can visit my site which is also my name to see it implemented and working.