You're going to have to edit the forum wrapper, which is relatively easy as long as you are familiar with the software. You will NOT have to do anything with FTP or the logo or anything like that...
I am unfamiliar with IPB, but I've done this before... In the administrator's control panel, try to find where you can edit the board wrapper files (or template files, whichever). From there, you must find the one that is the overall board header, and then you have have to insert the HTML/JavaScript ad code somewhere in the file.
If you want, I can try it -- but I will need access to your forum's administration panel.