If you use the admin->tools->banners to upload banners to your site you need to add a code snippet to your templates or pages where you wish these banners to be rotated.
Use the following code as an example
<? Banner::displayBanner('468x60');?>
Should your banners be a different size then just change the dimensions in the code. You can use this code in several places if you wish to display banners of different sizes in different portions of the template or use the same size banners in different places (for example in the header or footer). Please be aware that this will rotate ALL banners of the size denoted in the code snippet. If you wish to have a more targetted banner ad server we would recommend you consider installing and integrating OpenX