Adding my aweber popup script code to blogs mu

I want to add an aweber fade up box to blogs-mu but it doesn't allow the script to be added anywhere on the appearance settings so where do I add it in editor mode?
I am the only one using this theme on my multisite.
It has to be added within the <body>

</body> sections - which file do I go to, to find that? I looked through them and couldn't see it so I have obviously missed it!