I would think a better place to ask this would be the Joomla forums, http://forum.joomla.org/, but I must admit this question is also bugging, just this morning, I started using Joomla, and this very thing about how to replace the banner came up....
If you are adding an ad banner, you should use the banner component which is equipped with Joomla itself. When you are using a custom template, you need to configure the position of the banner component in order for the banners to show up properly. (This thread is a great reference).