I come from a background of coding my client website projects from scratch with MySQL and PHP. They are typically public facing sites with a mixture of static content, dynamic content plus a little functionality here and there (i.e. account, searching etc). Nothing too heavy.
So I generally code up a little CMS site to let them update what they need to, put it in a protected folder and that's that.
Now I'd like to use CodeIgniter and more of a MVC approach for my next site. Should I be doing anything to separate the CMS out from the rest of the site or is it simply another area (with its own controllers/models etc) and extra authentication?