[Jordan]

This depends, largely, on how you have built your CMS. You can make it as simple as including a header and footer on every page and the user could change these (this is how vBulletin works). You could pass all data to a template file that simply extracts and uses what data it needs (this is how Joomla! works). You could take a look at the smarty framework and replicate their template system (they use a bunch of .spl files or something similar that is very irritating to work with).

There are many more methods. John may tell you his method that he uses for his CMS.