It really depends on what you want the website to do. Whether you want it to act as a portal, or just a news-type site...or even a blog.
The first place you should start is http://www.opensourcecms.com and take a look at the different (free) platforms out there, and how they function. Once you decide on how you want your website to function, take a look at the cms's tutorials and/or documentation for customizing them.
After you settle on a CMS and have looked into their template systems, post your questions here, and someone is likely to have an answer for you. However, we cannot provide much help if we don't know which platform you're even interested in, first. 
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