Is there a guide to managing customisations on a site with an Azure deploy?

Particularly, the following scenario:

I have one CMS Instance with one site that is developed locally. The site contains some content, it's own styling and some custom logic (for special instructions on the shopping cart, for example). The instance is packaged and deployed. The site is now live and is further edited regards content on the LIVE site. Users are registering on the social side- and everything is perfect! :)

In the meantime, there is more custom development going on which introduces a new payment gateway (as an example). Also, the site's style has been updated and gone through a number of iterations. Let's assume we also had to test a hotfix and applied it to the local dev instance.

What's the best way to manage publishing those changes to Azure?
Re-packaging the site doesn't seem to be an option? Or is it?
Exporting the site, and then importing it will overwrite changes (content) on the live site?

In a shared host web application (what I'm used to), it's just a case of copying across the new binaries with new stylesheets/assets and running some SQL scripts on the live database.

How do I achieve roughly the same effect using Kentico/VS/KIM tools?

If I've missed a document/article that explains all this neatly, a pointer to that would also be just great :)