I'm not entirely sure what you mean, but I'll try to answer.
Yum is the back-end infrastructure for pulling updates and their dependencies from Fedora (and third-party) repositories. All other standard update programs on Fedora either run yum directly in the background, or use PackageKit to run it for them. All official updates are obtained from Fedora's yum repositories. So yes, all official updates are handled by yum, one way or another.
For "third-party" software, it's potentially more complicated. RPM-Fusion, Adobe Flash, Skype etc., all provide yum repositories for Fedora so that the same update mechanism can be used for the software that they provide, so again yum is used either directly or behind the scenes. It's possible to install software independently of yum though, and in that case any updates will have to be dealt with separately too. For example Firefox will handle updates of user-installed add-ons itself.