Yes you can change any CMS generated template graphics with your own using Illustrator and there are loads of info on this in the web just do a google search on the topic or use the one which gives info on making a button: http://www.adobepress.com/articles/a....asp?p=1623790
I wouldn't use Illustrator the same way I could use PhotoShop at generating whole web pages without any knowledge of coding but for backgrounds, buttons, all the rest of general web graphics including individual headers - footers and planing of a web site it is a great tool. Make sure you turn on pixel grid from Transform Panel before starting any graphic and always input your pixel graphic sizes on the top menu.