Hi Sam,
Footer, Header, etc., whole layout is defined in the master page template so you can customize it on your own. So I recommend you to convert you site completely into Kentico CMS which also save your time in the future... everything at one place.
Yes, controls could be made into WebParts, you can read more about it in the
DevGuide - Developing web parts.
But you can also use a lot of built-in WebParts of the Kentico CMS. E.g. Users permissions, log-in, log-out, whole CMSDesk layout, properties and a lot of more!
Best regards,
Martin Danko