Hello Tim,

Yes, it is recommend to put the site offline during these processes if you are making changes directly on the live server but...

The recommended scenario is to upgrade/update a local instance of the website everytime, e.g. on some local machine, after that completely test it and if everything is working fine then you can simply replace the live website on the production server.

More relevant information could be found in the One of hotfix packages and from version 6 you can also take benefit of using a competely automatic process via KIM (Kentico Installation Manager).

Best regards,
Martin Danko