[eluser]pickupman[/eluser]
Seems kind of backwards, but yes you can. Keep in mind there already a few great CMS platforms already built on CI which you could extend onto. Check out PyroCMS and ExciteCMS.
Wordpress is running php and mysql, so you definitely use both together. You will probably need some sort of .htaccess to keep things sorted out. I use them in separate folders on a site. It was easier to setup wordpress at the time, than develop a full CMS for a blog.